[Batman]

Cartek is junk with tuning.

My suggestions:
LS6 intake
Ported stock T/B
224-230 cam with a 112-114LSA, no split
Air lid
Kooks Longtubes W/CATS (The LS1 cars run alot better with Cats, unless it is race only I would keep them.
good Cat back (Magnaflow is my suggestion, I had LM and the Mag put down 12 more RWH and didn't make your ears bleed)
Nice set of Stage II heads ( I suggest Rapid Motorsports or AFR)
NGK TR55 plugs
Good spark plug wires
4.10 gears for a M6 and 3.73 for an A4
Get your car tuned!

Things I would not do:
-Aluminum intake (weiland and BBK) No gain over an LS6 unless you port it and it holds more heat then the LS6 one does.
-You already have 1.7 Rockers, 1.8's I would stay away from, most of them have clearance issues with the valve covers
-MSD ignition - unless you are planning an all out race motor there is no reason to shell out $600+ for MSD coils and then another big chunck of change for the tuner. Stock Gen III Ignitions are awesome and don't need much help.

Bigger isn't always better with an LS1, I have about 20 different setups on mine and I was busting up heads/cam cars with just a cam and 4.10's ( a small cam at that. Do your research and decide if you want the all out track car or a killer street machine.