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Are you talking about a complete LS6 or LS6 bottom with LS1 top? If the lader, then there are a few little changes like rockers and not sure on the rest. Should upgrade to a LS6 clutch and slave and of course, tuning.
I have went through the process a couple of times.
From: "Second place is just the first loser" Edmond, Oklahoma
It works great........need to reflash the pcm, obviously. My 136,000 mi 1998 A4 coupe got a new 04 LS6 about 3,500 miles ago. I installed a 3.73 rear end and autocrossed the car for about 1 1/2 months before the high mileage 4L60E tranny died.........................but, I had anticipated that and had an 18k mile used one in the garage waiting. I also had a new torque tube on standby. I haven't dyno'ed it yet, but with bolt-ons (BPP bottom breather air intake, halltech air bridge, Borla 4tip stingers, Shaner polished and ported TB) it's probably in the 370 rwhp range and torquey as heck. It makes a really fun daily driver. On the way back to Oklahoma from Denver, I kicked it up to 170 mph in eastern Colorado and it was still pulling hard. With the exception of that mad minute, I averaged about 70-75 and got an honest 25mpg. I run stock Z06 wheels, Z06 torsion bars, 2003 Z06 shocks. After Christmas, I'm gonna install HUD.