I've got a 2005 496 with 110 hours on it. Just installed a whipple and took it for the maiden voyage. Lots of new power - gained 14 mph over stock. (very impressive) However, as I was check for any leaks or issues, I noticed a random low end knock. It is not exhaust flappers and it does not appear to have anything to do with the supercharger itself. It seems to be coming from the lower front of the block. Almost sounds like marbles in my water pump. However, it will idle for up to 20 seconds perfect with no noise, then it comes back. It is very random and does not seem to follow a pattern with any of the belts or rpm variations. I had to run it for several miles to get back to the launch and it didn't get worse but I can't figure out where it is coming from? Any ideas where to start?

Sounds like rod bearing. I had the happen to my 454 this last summer.

Ive seen guys bolt blowers on before, get some detonation, and pound the rod bearings.