hey i just saw your email, sorry but i am not familiar with Covert Performance twinscroll kit? (never heard of them before). It is difficult for me to troubleshoot since i am not familiar with their product. my input:
-that is the laggiest twinscroll 35R ive ever seen, there has to be a leak (boost leak or exhaust leak, pre turbo) or the header must have been poorly designed. Your spool is at least 1000rpm later than it should be. I recommend a thorough boost leak test, and examine the headers for cracking or the wastegates for leaking.
-we machine the Borg Warner S300SX turbochargers so that it is a true 3" vband and a direct bolt-on for your GT35R.. no modifications required for the downpipe
-if you can post some pictures of the turbokit, it might help me to get a better idea on whats going on and provide some more suggestions or recommendations