What is your boost? The Thrasher will command more boost than the stock chip and if you already had it turned up you may be too high. Do you know what knock sounds like? Are you getting any bfore the popping?
Set your iac and tps. Instructions are on gnttype.org. May not be your problem, but my Thrasher worked much better after those adjustments.
I was thinking that the Thrasher should be 42 psi, but maybe it was 45. Check to be sure.
You certainly should get a fuel pump, scan tool, boost gauge and other basic mods to support any performance upgrades. I would think that the stock pump would be OK with the Thrasher at 16 psi and lower. Mine was, but it only had 22K miles on it at the time.
Double check your chip install. Make sure it is in evenly and fully.
Clear your ECM. I don't know if driving around and letting the chip/ECM learn about the car will make a difference, but it won't hurt. Not a reference to the post above, it was posted while I was typing.
Good Luck,
Tom