Redneck

Been surfing the forums for weeks and haven't found exactly what I'm looking for.

Car:
2004 Rx8, Manual Transmission, Ran on premium fuel and premix since i have owned it. 85,XXX miles on the body, About 12,XXX on the engine, Oil changes done every 3k miles.

Service history:
75,XXX:(Purchased Fall 2016) New engine bought from Kurt Robertson and installed by previous owner, aftermarket body kit, aftermarket magnaflow single exhaust.
Car ran like crap when I bought it.
(Post Purchase) Clutch replaced, New upgraded starter, Clutch master cylinder replaced, SSV pulled and cleaned and grounds checked by Kurt Robertson. SSV and VDI solenoids replaced. Aftermarket AEM style air intake (Yes with air screens and line capped)
Other things done since purchase: Oil pan pulled and resealed, Install of amp and sub, A/C delete (Was never fully installed after engine swap), Oil catch can (installed while car was sitting)
Issues:
Around 85,XXX miles i was out on a drive, coming home from work. I stopped and got gas. It had a slower start than normal at the gas station, but i got it going. Then headed home, stopped for some groceries. Couldn't get started outside of the store. Cranking to just below 500rpm. And that's when all the issues started.
Since then, i have not been able to hot start, the car runs really rough, exhaust is choppy sounding, slow cranking, runs really rough, low idle when hot (750), quite powerless.
The most unique and consistent problem other than powerlessness is a lag at 4k rpm and then a slapping noise 4,500 to about 7k rpm. This is not MIAC, its not made by the exhaust and only occurs under load. The car misfires at 8k rpm but not before.

Codes:
I've been collecting all kinds of wacky, random, and one time codes. Codes like "Throttle position sensor (A and B) Low circuit" (Throttle did stop working at that time, but worked after reset), to MAF codes, "idle air control B low circuit." Most of these codes go away after clearing the codes, even when i cycle the engine.
Consistent codes: Misfire cylinder 1, The original code was for an SSv solenoid

All information collected after I stopped driving the car:
Pulled cat and checked it, New coils, plugs cleaned and checked for spark, SSV actuator replaced (Mine was making the ticking noise.), Oil drained and checked for metal shimmer in case of spun bearing. All air solenoids tested (SSV had to be replaced)

I have attempted a compression test with a standard compression tester but it didn't seem to have rational numbers. front was like 30, and rear was 60, but if the eccentric shaft sensor was plugged in the rear would throw out 90

I cannot seem to figure out the slapping noise, it sounds similar to exhaust braking and some larger trucks, or like a plastic piece being slapped by a fan (I do not recommend sticking things in a fan to get an idea, and yes i checked my cooling fans they seemed to be spinning fine.)

Hopefully I can get it into a shop, Kurt is too busy at the moment to help.
Thanks for the read.