I would run the stock LS1 or LS6 intake on a budget turbo LS1. LS1 intakes are a dime a dozen and a used LS6 intake sells for about $350 shipped all day long. No point in going carbed IMO. There are quite a few people making 1000rwhp thru them with ported stock TB's going low low 9's in 3200lbs+ cars..... they work. Just have enuf injector!
Tuning for the stock computer is typically done with either LS1 Edit or HP Tuners. You can dump the MAF sensor and go full speed density. The LS1 computer is miles ahead of the GN ECM.
Best bet would be to install some 6.0 heads on the LS1 shortblock. They will lower the compression to be boost friendly. GM "MLS" head gaskets is what most run and a set of ARP head studs are good insurance. Stock LS1 pistons seem to be the weak link and beyond 550-600rwhp you are on borrowed time as the ring lands seem to fail.
There are a few guys running $200-300 "OBX" generic eBay intercoolers making 700rhwp+. I would plan on plumbing one into your setup.
LS1 block after lots of street miles making 700rwhp+ seems to get the bores out of round and you lose ring seal. In a race car application this will probably never happen and a few have made 1200hp+ going low 8's at 170mph+ with stock crank/hi perf rods/pistons. The LS2 alum block (4.0" bore) with stock crank, cheap $400 Eagle rods, Diamond pistons has been proven to 1000rwhp reliably. In about 1 month the '07 Escalade alum block will be out with a 4.065" bore (416ci with 4" stroker crank).
LS1 technology is pretty awesome with lots of interchangeability, individual coil packs per cylinder, strong factory cranks, and very good factory flowing heads. For $2200 you can get an AFR head that flows 320cfm and has a thicker deck than factory. 1000rwtq out of the box potential. or port the factory 6.0 castings which have been 8.0's@170mph+.