Also I forgot, you are going to need to build some of your own "special" tools to work on the ally.
If you have some metal, a solid table or engine stand, and some good fab skills, you can build a bench stand for the allison. These stands bolt to the PTO housing on either side of the ally (i always bolt it on the non-NSBU side). Otherwise you can stand it up on the bell housing to work on the C4s and stand it up on the rear housing bracing it with 4x4s to remove the C1/C2 hub, pump and replace the C3s.
Another tool you will need to make is something for compressing the C1 springs. There is no way you will compress them without the allison tool or one that you made by yourself. I used a piece of 4" exhaust pipe, then cut a notch out of it to get the snap ring pliers in there. If you have a press all you need is the exhaust pipe, but if you dont have a press or access to one you can build one like mine and it will work great.
Finally you will also probably need to build a tool to keep the main shaft seated correctly. Its simple something that bolts across the main case on the bell housing side with a piece of redi-rod and two nuts to adjust and hold it in place. Not getting this shaft seated right will cause lube holes to be misaligned.
Its also very important to get all of the torrignton thrust bearings installed in the correct orientation, failure to do so means big issues.
Another note is that it is normal for the rear housing to sit up somewhat, but if there is a big gap, something isnt right.
KEEP THINGS CLEAN.
And finally, CHECK CLEARANCES. These will let you know if something wasnt done right.
Here are some pics of my tools on my "trans" bench.
