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MT-82 Trans Will Not Enter Engine All the Way! About a 1/2" gap

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Hey folks, I'm having some serious trouble mating my transmission to my engine. Here's the backstory:
OEM clutch overheated a few weeks ago so I'm upgrading to McLeod RXT twin disc unsprung hub + McLeod billet steel flywheel (part # 6435825M). Since I'm in the trans, I'm replacing pilot bearing with Ford Performance High Load pilot bearing (M-7600-C)and TOB with Ford OEM throwout bearing (BR3Z-7A508-B) and installing ARP flywheel bolts (156-2801), and McLeod stainless steel clutch line. Removal of old parts and installation was great. At this point, I have the new clutch and flywheel in, the new pilot bearing and TOB installed.

I cannot get the transmission to mate to the engine. I have about a 1/4 to 1/2 inch gap still to go. I can draw it in with the transmission bell housing bolts if I really try but as I've heard a million times, I never want to do that since if the transmission isn't slipping in nicely by itself, it's caught up somewhere. As I turn the engine crank, the flywheel and clutch spins so I know the input shaft is engaged into the twin clutches and flywheel. The transmission is not caught up on the headers or anything outside the case. The transmission is also inside both the driver and passenger side dowels. The transmission has been in neutral (if that matters). We've wiggled the trans up and down, left and right, and pushed from the rear of the transmission even with the manpower of legs about 1000 times with no results. The clutches are perfectly aligned using the McLeod plastic clutch alignment tool as we've loosened the pressure plate and re-aligned the clutches and tried again with no luck. This leads me to believe that the pilot bearing is either not installed correctly (which I don't believe is the case) or the inside diameter of the bearing is smaller than required (factory defect of some sort) making it extremely hard to insert the input shaft. Or maybe the FP high load pilot bearing is not meant for the stock MT-82 input shaft (even though it is listed as good to go).

I'm looking for any ideas of why my transmission is not slipping in with ease based on the info above. I can provide any pictures necessary.
Thank you to everyone that can help me out here. Looking forward to hearing the thoughts.

Car Specs: 2013 Mustang GT with Gen 1 5.0 + 2013 stock MT-82 6-speed manual transmission
 
1,294
1,300
Exp. Type
HPDE
Exp. Level
5-10 Years
Lenoir City TN
Check the diameter of the input shaft and the pilot bearing with a dial caliper just to make sure that you didn't get something off spec. It sounds like the clutch isn't centered with the pilot bearing so the input shaft is hitting the shoulder of the bearing instead of sliding in. Did you lift up on the end of the alignment tool to make sure it didn't sag when tightening the clutch? If it sags the disks are in alignment but not perfectly centered with the pilot bearing.
 
Check the diameter of the input shaft and the pilot bearing with a dial caliper just to make sure that you didn't get something off spec. It sounds like the clutch isn't centered with the pilot bearing so the input shaft is hitting the shoulder of the bearing instead of sliding in. Did you lift up on the end of the alignment tool to make sure it didn't sag when tightening the clutch? If it sags the disks are in alignment but not perfectly centered with the pilot bearing.
I will check the diameter. At this point, I'm ready to remove the new pilot bearing and install a new new pilot bearing that is not the high load version as I suspect this is a pilot bearing issue. I did lift up on the end of the alignment tool to make sure it didn't sag when we loosened the pressure plate and re-torqued. So that is not the issue.

Maybe I should look into buying a metal clutch alignment tool...
 
1,294
1,300
Exp. Type
HPDE
Exp. Level
5-10 Years
Lenoir City TN
The plastic alignment tools work, but are not the most precise. A steel tool does fit better. The best alignment tool is an old input shaft from the same model transmission.
 
Does your plastic alignment fit the pilot bearing snugly?
It fit very very snug the first time around when I did not push up on the clutch alignment tool when tightening the clutches. After loosening the pressure plate, putting upward pressure on the alignment tool, and re-tightening the clutches, the alignment tool slips in much easier. But it is still a rather snug fit without any wiggling around once it's in there.
 
1,294
1,300
Exp. Type
HPDE
Exp. Level
5-10 Years
Lenoir City TN
The alignment tools are sized for the pilot bearing. If it fits snugly I wouldn't think there is a problem with bearing diameter. I had a similar problem when swapping my MT82 for the Tremec T56 Magnum XL. I couldn't get it in the last 1/4". It ended up being a bad alignment tool. I was accidentally sent one for a Chevy pilot bearing which is slightly smaller in diameter. The input shaft was catching on the shoulder of the pilot bearing and wouldn't go in. Once I got the correct tool (steel this time) it slid right in.
 
The alignment tools are sized for the pilot bearing. If it fits snugly I wouldn't think there is a problem with bearing diameter. I had a similar problem when swapping my MT82 for the Tremec T56 Magnum XL. I couldn't get it in the last 1/4". It ended up being a bad alignment tool. I was accidentally sent one for a Chevy pilot bearing which is slightly smaller in diameter. The input shaft was catching on the shoulder of the pilot bearing and wouldn't go in. Once I got the correct tool (steel this time) it slid right in.
That’s quite interesting. I’ll order a steel alignment tool as a start and hopefully that’ll give me some results. Thanks!!
 
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Agree with all the above, it always pays to slide the new TO bearing over the trans sleeve, and do the same with the pilot bearing. The plastic alignment tools can be sketchy, in the old days we would slightly depress the clutch and the trans would slide in, if it was slightly mis aligned.. I think you could do that as well, but you would have to think it through first. I think it will try to push the trans back out in the current configuration. You might try putting some longer bolts in to hold the trans, slightly apply some clutch pedal and have a relatively large guy shake the trans and try to align it better.. that just might work, because the TO bearing will push out against the longer bolts. You are just trying to line stuff up, then let off and try pushing it all the way in.
 

Dave_W

Cones - not just for ice cream
1,062
1,388
Exp. Type
Autocross
Exp. Level
20+ Years
Connecticut
If the problem is the nose of the plastic alignment tool being small for the pilot bearing, would wrapping it a time or two with electrical tape help?
 

TMSBOSS

Spending my pension on car parts and track fees.
7,615
5,385
Exp. Type
HPDE
Exp. Level
10-20 Years
Illinois
BS1
Back in the day we bolted the bell housing with the throw out bearing up before the trans went on. That allowed us the flexibility to push the clutch in and slide things around for final alignment. Today, we risk over extending the slave cylinder on the throwout bearing if we are not careful.
Unfortunately pulling the trans out and realigning after confirming everything fits, throw out, pilot and discs may be unavoidable.
 
1,294
1,300
Exp. Type
HPDE
Exp. Level
5-10 Years
Lenoir City TN
If the problem is the nose of the plastic alignment tool being small for the pilot bearing, would wrapping it a time or two with electrical tape help?
Yes, if that is the issue it can help. When Mantic sent me the GM alignment tool they said I could wrap it in tape to build up to the correct diameter. Silver Sport Transmission is only 1/2 hour from my house and had the correct steel alignment tool in stock, so I ran over there instead. What they sold me looked like an input shaft with the gear cut off. Fit perfectly and the trans slid in with minimal coaxing. Took less than 10 minutes and it was flush with the engine.
 
BS1
Back in the day we bolted the bell housing with the throw out bearing up before the trans went on. That allowed us the flexibility to push the clutch in and slide things around for final alignment. Today, we risk over extending the slave cylinder on the throwout bearing if we are not careful.
Unfortunately pulling the trans out and realigning after confirming everything fits, throw out, pilot and discs may be unavoidable.
This is exactly the issue I am having and the thought process I've went through. I've went through 2 brand new throwout bearings already by pumping the clutch pedal just a few times since pumping the clutch pedal on these new hydraulic systems pushes the piston out of the TOB rendering it useless. So I'm not able to push the clutch pedal in or out unless it's sitting on the clutch fingers, which is a risky game when the trans is not bolted up since it'd be hard to tell when pushing the clutch pedal in is too much compression on the TOB causing the TOB to release from the clutch fingers and pushing the TOB piston out again.
 
6,676
8,786
This is exactly the issue I am having and the thought process I've went through. I've went through 2 brand new throwout bearings already by pumping the clutch pedal just a few times since pumping the clutch pedal on these new hydraulic systems pushes the piston out of the TOB rendering it useless. So I'm not able to push the clutch pedal in or out unless it's sitting on the clutch fingers, which is a risky game when the trans is not bolted up since it'd be hard to tell when pushing the clutch pedal in is too much compression on the TOB causing the TOB to release from the clutch fingers and pushing the TOB piston out again.
yep that's the problem with the new setup, that's why I suggested longer bolts, to get the TO to push against something. The steel alignment tool is the real answer, I keep several dead ones lying around just for that reason, and, just like the OP sai, they have the gear torched off of them.
 
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556
If the slave cylinder (not TOB) has fluid in it, the transmittion will not slide all the way in. You will need to use bolts to very carefully pull the transmission in. You will not be able to turn the bolts by hand after they start. There should be very little resistance when turning the bolts with a wrench. Fluid will run out of the slave as it is compressed. Do not try to depress the clutch and actuate the slave without the transmission being fully seated or you will damage the slave.
 
1,294
1,300
Exp. Type
HPDE
Exp. Level
5-10 Years
Lenoir City TN
If the slave cylinder (not TOB) has fluid in it, the transmittion will not slide all the way in. You will need to use bolts to very carefully pull the transmission in. You will not be able to turn the bolts by hand after they start. There should be very little resistance when turning the bolts with a wrench. Fluid will run out of the slave as it is compressed. Do not try to depress the clutch and actuate the slave without the transmission being fully seated or you will damage the slave.
That has not been my experience. When I reinstalled my MT82 I bench bled the slave cylinder and it slid right in tight, but it did shoot some fluid out as the slave cylinder preloaded. It was a bit of a mess and I had to clean it up. I learned from this and when I installed the T56 Magnum XL I once again bench bled the slave, but this time when I was about an inch from tight to the engine I snaked the clutch line back down and attached it before sliding it in flush to the engine. No mess and it went right in. I did not have to use the bolts to draw it in with either transmission.
 

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