RedLined

Hi guys been having this issue for a few weeks now and I can't figure it out. Car is on 05 Ion RL. It started with a p1182 and then went to p0068 under boost. A few days after I got those codes I cleaned everything with no success. I then got a code for the tb and one for the scip so then I replaced the maf, map, tb, and the scip. The only thing I ever got strange readings for while doing my trouble shooting was the scip. The symptoms the car has starting at a coolant temp of 140f are: negative idle timing, what seems like a low scip reading at idle (8-9 psi), low vac at idle (17-16 inhg), slightly higher than commanded idle speed, and a high idle speed on coast down. There are no vac leaks. I've checked every line, fitting, and connection. Bypass valve and actuator are good.
Mods are tvs, injectors, dual pass, ls4 tb, k&n typhoon, phenolic spacer, zzp lt header, zzp 3 inch exhaust, and running e47.
Also, not sure if this is related but every now and then on a cold start theres an audible rasping/grinding noise like something is moving quickly without lube and then goes away almost instantly. Doesn't last more than a second. Oil is new, plugs are new. Timing chain was replaced in the summer along with valve springs, rockers, and lifters. O2 sensor, thermostat, and fuel filter were replaced about 18 months ago.
The car only seems to act strange once it's it hit 140f which I'm guessing is when closed loop kicks in. Fuel trims at idle go back and forth between - and + but they're fine while driving. I've flashed the pcm to the last tune before the issue with no difference.
At this point I'm out if ideas and considering a wiring or pcm issue.