I don't wrench myself, I paid a member on V6P to do it. But I can give you some info.
Mechanically, everything bolts right up. Axles and everything.
Electrically, you are going to need to do some repinning on the harness. I don't know any info here. Maybe the Temp gauge, Reverse lockout for sure, some other things I just don't know about.
Those 5 speeds from 01-03 Acura TL/CL had issues. 2nd gear oil jet If I remember. In the 03-06 Hondas they beefed up the 5-speeds a little bit.
Grab a 5 speed auto from an 03-06 Accord(the later the better as they worked out the bugs in it) or 04-06 TL-s. Bell housing bolt pattern changed in 07 so only go up to 06. The "tip tronic" or manual selection will work, no special wiring needed as it is controlled by the ECU.
Engine Harness can be from 01-03 Acura CL or TL base model or Type S.
ECU same as above 01-03 Acura, but I recommend you try and find one from the latest production as it is the one I use:
ECU #37820-PGE-A61
the A62 was the last one they made as far as I know, if you can find it grab that one.
You will lose TCS as the systems are different on the Acura vs Honda. This will most likely give you the "phenomenon" of the tranny hanging in 2nd gear when you spin off the line. I don't know if anyone has figured it out, but we think it is in the ECU. We just let off the gas and let it coast, then it will shift into 3rd.
Hood clearance is an issue - lower the sub frame 1 inch or use that 3.7 SH-AWD intake manifold set up. If you want you can do the ghetto method by cutting the hood supports, but It's not recommended due to safety reasons
You can reprogram the key to the ECU or just ditch the Immobilizer.
CEL will always be on due to the different TCS systems.
If you want to go manual you can use these:
03-06 Accord V6 - NO LSD
04-06 Acura TL Type s - DOES have LSD
03 Acura CL-s - LSD? not sure.
If you go manual and want to use headers, you need the rear primaries with the Bend in it to clear the manual tranny mount: XS headers and some EBAY no names are out there. Have someone RE-weld the welds on the primaries before you install them as they always crack down the road.
** I always recommend to do a fresh rebuild unless you know for sure that engine is solid. That way you can go ahead and port and polish the intake and heads also.
This is probably not everything you need to know or do...
Good luck.