I'm one of the few people here that actually owns and drives an A3. I heard all the usual stuff about the truck having a crap engine and junk trans. None of it is correct and most of it is not true. As far as the trans, check the fluid level first. The dip stick is under the passenger side matte.
The trans service kit is available from any truck parts place, the external trans filter is a Baldwin, the trans can be serviced and refilled with ATF instead of the motor oil the Army uses with no problems. The shifter is dirt common as well and the linkage is pretty straight forward.
Any one with experience on commerical trucks can give it a once over with no problems. The engine is in thousands of things from RV's, generators to school buses and GM Top Kick trucks and many have hundreds of thousands of miles with no problems. Most of the rest of the truck is straight M35 and can be found anyplace.
I had my truck serviced by the local Cat dealer after I picked it up. He owed my brother a favor so it got cheaper. I had them service the driveline, change fluids and do an overhead on the engine. The overhead by the way is recommended after the forst 500 hours of engine operation and every 1000 hours or 100,000 miles after that. So for most A3 drivers it is a once in a lifetime tune.
The Cat dealer had no problem finding anything he needed to get my truck squared away in the local area. They even had the engine profile information in their computer in the mil-spec. Mine runs great and flew through emissions with no problem either.
I then drove my truck 2500 miles home and did not use anything other than diesel and a quart of oil. Some of the help and offers of assistance I got from a few folks here made the trip al lot less scary knowing there were a few friends along the way if disaster struck.
Erik's Military Surplus was and is a great place for A3 parts. Erik has a ton of good information and is will to share it for free. His prices are reasonable as well. Erik answered my power steering questions asap and that allowed me to get things adjusted before I hit the road. He also had all of the bits and pieces I needed once i had some time under my belt with the truck.
As far as CTIS, mine has been trouble free ever since I cut it off. It really is not worth messing with most of the time. I drove trucks with it on active duty and nearly all of them had problems as well. Just by an air hose to service your truck off the glad handle like everyone else.