I know this is old but I will answer this question for any future reference.
ported/polished ls1 heads will flow very close to ported polished LS6 heads. Its all about the port work. Advanced Induction, Texas-speed & performance, AFR, TEA all are very reputible for there programs. I would honestly send your stock heads to one of the listed above and tell them what the purpose of the car is, what type of cam you plan on running, what to of power you want to make.
Once the LS1/LS6 heads are cnc'd and polished, there is minimal difference's. The flow numbers will usually be between 305-315 @ .600 lift on a 3.905 bore. A ported 98 head will out flow a stock LS6 head. The best option to go with is a ported/polished 243 head (if you are not building on a budget), but you can not go wrong by any worked LS head. If you have the 97-98 perimeter style head, it may be best to stick with those as you will have to buy new valve covers and coil brackets to run a LS6 head.
Here is a great write up on how to make 500rwhp with a H/C/I 346 LS1. This write up should give anyone the base knowledge needed to build a combo that works as far as knowledge about the heads, cam selection, intake, and custom exhaust set-up
http://www.ls1tech.com/forums/....html