Good Evening Everyone!
This is my first attempt at pulling and re-installing my transmission (slave cylinder needed to be replaced). I feel like I am so close so wanted to ask for some advice from those of you who have been working on these for many years. For reference I have the 4.9L and manual transmission (M5OD). I have gotten far enough for the face of the slave cylinder to be flush with the pressure plate (as viewed through the bell housing) but I cannot seem to get the transmission to budge any further. When viewed from behind, the bolt holes appear aligned, and I also appear to have up and down alignment as well. Is it possible the splines have gone out of alignment? I was hoping the fact that I can see the slave cylinder face touching the pressure plate meant the splines had gone in far enough to be engaged properly with the clutch plate. Thank you so much for all of your help!

 

My guess would be the transmission shaft is not engaging into the pilot bearing in the back of the engine. I assume you used the alignment tool that came with(should have came with) the clutch kit?

 

Not uncommon to have to run the trans in the rest of the way with the bolts
You are down to just the pilot bearing right?
In the old days you could hit the clutch and the disc would move ever so slightly and the trans would be home in an instant
Just hold your mouth right and run it in the rest of the way with the bolts

 

So I gave it another try this morning and still no luck. I removed the slave cylinder (concentric) to see if it was pushing against me but when I tried aligning the transmission again without the slave cylinder it stopped the same amount of distance away. Now wondering if it is indeed an alignment issue I removed the pressure plate and clutch disc and when I began to loosen the pressure plate bolts I noticed the alignment tool was much less stiff moving in and out and actually went in further. So new question for when I go to re-align everything (since I had an issue the first time), is there a special trick to using this alignment tool in the process of mounting the clutch and the pressure plate because something clearly shifted when I did it last. Thank you everybody!

 

The alignment tool holds the clutch disc in alignment with the pilot bearing in the back of the engine. The proper way to use the alignment tool is simply insert it through the clutch disc and insert the tip of the alignment tool into the pilot bearing and then bolt the pressure plate into place before removing the alignment tool. Then you should be good to go mounting the transmission.

I assume you didn't do anything with the pilot bearing. If so make sure there are no knicks inside the pilot bearing or the outside of the shaft that fits into the pilot bearing.

 

The pilot bearing should have been replaced and a new clutch installed IMO anytime the trans is removed or the slave replaced
Murphey's law states the clutch will go out soon after the (one forth) of a clutch repair
The alignment tools have enough play that unless you hold the disc right in the middle of that play you will be off a (1/16) or so
The transmission when removed could have moved the disc slightly and now it is off center under the pressure plate
A bit hard to get your hands on but,
If you use one of these (1st gear) input shafts, there is no play and the job goes easier in most cases

 

 

Success!!! I pulled the pressure plate off and realigned using the tool again but this time being more aware of where my tool was and making sure things didn't move once I had it all set. After that the transmission glided right on in with very little effort! I did replace the pilot bearing as well with the new flywheel, clutch and pressure plate. Thank you so much for all of your suggestions, I really appreciate all the help and guidance!