Manual transmission removal problems

[dramm18]

I am new to this site and to forums for that matter but i have had a lot of friends get help from forums and i did not know if anyone has gone through this situation before.
I have a 2006 xterra 2wd 6speed manual and about a week ago the clutch went out. i have never pulled a transmission before but i have done plenty of other replacement jobs on this xterra and i figured i could swap out the clutch myself. the point im at right now is everything is free from the transmission the engine is supported and the transmission is on a transmission jack which i can move about 2" from the engine and thats it. i noticed the cats are pinching the housing a little bit but it looks like there should be enough room for the transmission to clear. i have done everything the chiltions has told me to do but she still wont come back.
i was wondering if anyone else has done this job and could offer any advice as to what could be hanging this transmission up?
all help is appreciated!!! and thank you

[Ozzie]

If the engine and transmission have been jacked up to (slightly) different levels, then the transmission input shaft could be bound up on the clutch.
Imagine trying to pull a key out of a door lock slightly sideways, instead of not directly in line. It is harder to get the key out!
Try raising or lowering the transmission a little to see if that makes it any easier.
Also, have you removed/dropped the tail shaft? (You didn't mention if you had or not)

[dramm18]

yeah i have removed the drive shaft, exhaust (from cats back), and cross member that supports the extension housing of the transmission. it will move back about 4 to 5 inches now but it is still getting bound up im thinking i have the engine too high still and when i try lowering the transmission it is getting held up by the input shaft so im thinking of trying to lower the back of the engine more but im worried about bending an engine mount.
How far could i lower the engine and not put too much stress on the engine mounts?

[Ozzie]

I suggest just try lowering the engine, while keeping an eye on the mounts.
If you are worried that they are coming under too much stress, and the transmission still won't move, you may have to undo the mounts and give the engine a bit of support from above, with a block and tackle or an engine hoist.
This will give you a bit more movement and hopefully allow the transmission to come free.
Good luck, and let me/us know how it goes! *fingers crossed*

[dramm18]

got the transmission out finally all i had to do was to loosen two of the nuts of the right cat and that gave it enough clearance for me to be able to work it out. the new clutch is in and torqued down and im in the process now of re aligning the transmission to get it bolted back in and im finding out how much of a pain that is.
any tips on lining up the input shaft of the transmission to the clutch disk and getting this thing back on?
as always thanks for the help