Just and update,
I had a case of H1N1 about 10 days ago, so progress has been slow on the reassembly.
1. Getting the transmission out is a monster-- There is very little bellhousing and tunnel clearance when moving the trans back to clear the clutch, and the engine wants to tilt forward slightly as you begin removing. Has to be the tightest fitting tranny I have wrestled to date! Oh, it is also the heaviest and definitely lets you know it when it falls on your chest!
2. Do not remove the bellhousing, unless you want an upclose and personal look at the internals of a TR6060 and have a couple of spacers and races fall out

No big deal though if you do. Definitely not like the older t56's
3. The Borla headers slid in like a glove and tuck up tighter to the floorpan than the stock exhaust. They barely dip lower than the front subframe. Unless you are Houdini using all the locking clips on the Stage 8 bolts that are supplied is impossible. But, I do like the design and being able to use and allen wrench to tighten some did help alot!
4. I used the stock MLS type manifold gaskets rather than the supplied header gaskets. I just used high temp RTV around the flanges. They seem to be a better quality and I definitely do not want to change blown header gaskets anytime soon! Port match on heads and headers with stock manifold gaskets is excellent.
5. The Ram Twin Disc set-up is so much larger than the wimpy 8"ish clutch that it is replacing. The billet aluminum flywheel is definitely nice also. I am mailing my visibly warped and heat checked flywheel and disentigrated clutch to the lady at ford who denied my TSB claim. Clutch was slipping and free revving when under any boost at all...
6. Easiet way to measure for Throwout bearing clearance is with a cheap tool from speedway motors that circle track guys use to measure clearance. I highly recommend using this tool, rather than holding a straightedge and a caliper like in the directions.
7. Use the proper pilot bearing puller... I didn't and ended up spending way too much time cursing and beating on the stock one....
8. I still haven't fully gained my strength, so I have been putting off installing the transmission for a few more days or maybe until this weekend.... Damn thing is heavy. I could have used my friends lift and tools, but I wanted to go old school on my back to see how difficult it is compared to an old fox body. Now I wish I was on the lift with a tranny jack, so I may load the car and parts on my trailer and take it to his shop to button up.
9. With the headers on, access to oil filter looks better and transmission and starter can easily be serviced as stated by Borla.
When all is done, I will try to upload some pics I have taken during my backyard TSB.
Maybe this will help out some DIYers
Caleb