Ok here is a little update:
* Checked JR header for any visual leaks - nothing. (might take off my Monsterflow CAI, and go back to the stock airbox* so I can actually hear if there are any leaks)
* Put a brand new Magnaflow cat on - no change.
* Changed out the TPS from a low milage miata (did not go by the book to correctly adjust the TPS, is it detrimental?)
* Took off the midpipe to weld any possible leaks on the resonator.
After all of the changes I am still experiencing low accelerating / bogging / and knocking.
Next thing I may wanna try changing are park plug wires and plugs.
I also got some error codes now!
P0120 - TPS error
P0510 - closed throttle position switch.