I've heard that about losing bottom end power but if you believe what this CarCraft article says, it looks like there is very little difference in reality. According to the article there was very little change from vette manifolds to 1 5/8, 1 3/4, or even 1 7/8 headers. Of course that is on a bone stock LS1. So, it may stand to reason that an LS with ported heads and some cam may see more gain...but at the same time it didn't see any real loss under the curve.
http://www.carcraft.com/techarticles...e_header_test/
I pan on doing cnc ported heads and a Lingenfelter cam and don't want to feel like I left any on the table with this engine. My 56 is all stock and has the vette manifolds and I know it runs well, but the power is lacking IMHO. I am amazed how many people see the 5.3 in there and say "wow, I bet it's fast!" and internally I'm shaking my head. I want my 69 to outrun my 56 with one arm tied behind it's back when it's done. It will have more engine, more gear, more stall, and bigger exhaust. Can't go wrong with that recipe, can I?