I'm going 94' A4 V6 to LS1 6speed. You'll have the issue with the fuel return... you can go 98' vette rails, I did Aeromotive rails + regulator, and tapped into the hard lines under the driver with adaptor and/or flares and tube nuts. For the tranny, you'll need an LT1 6speed crossmember, NOT an LS1 crossmember (the bolts on the body are in a different location than an LS1 car, but at the same spot for the tranny. Stick with your body style for cossmembers just get the right standard or auto crossmember.) You'll have to cut the hole in the tunel for the shifter and a hole for your clutch master cylinder behind the pedals on the bottom driver side of the firewall. Obviously, look for some 6speed pedals, all this assuming you DO go 6 speed. I had an LS1 harness modified by Speartech (a sponsor) to plug and play with my body harness, so no wiring mess. Left my AC as is, (not running yet, so we'll see) but will try and adapt to use the LS1 compressor. I replaced my radiator for an LS1 radiator, but..... you have an LT1, whereas I had a 3.4 V6, you may not have to. I have a stock V6 Mickey Mouse single cooling fan. I'm leaving it for the time being, but realize that this is only temporary, a real fan setup, wheather its stock LS1 or aftermarket will have to be done. Also your air intake setup will be a BITCH. If you put an LS1 airbox in, your hood wont come even 4inches from even catching the latch, so you'll still be using your radiator support (a front end LS1 conversion would eliminate this intake ****, i went the hard way so i hope u do to.). You've got to get air from the stock location, I'm using an LT1 1LE 90degree hose that's oval shapped, so I SHOVED it over the LS1's round throttle body. The other end is round so the MAF will fit easier. Also, I stongly suggest you get an ABS delete block. This will make routing whatever type of cold air intake you do ALOT easier. The K&N LT1 intake can be made to work with out removing the ABS, but whatever kind of intake you end up doing (even K&N) its alot easier with the ABS module GONE. Thats all off the top of my head, let me know if you have any questions.
PS... I'm currently at $7000+, but I did alot of extras (cam, fuel system, LS6 intake and valley cover, throttle body, eletric water pump, long tubes etc....). But be forwarned, it get's expensive, and for many, its a better idea to just by an LS1 car. I'm still happy with what I've done though. So, good luck.