after sitting for 5 hours my car went from running great to running terrible

Are you saying it idles fine as a 4 cylinder;running on the drivers side only. And all the plugs are still in it?
Single or dual exhaust?
Sounds like #6 intake is not closing, and pulsing back into the intake. Put a vacuum gauge on it. Running with/without, #6.

single exhaust, looks pretty cobbled together. its an EGR engine also, no vacuum line going to the EGR valve

and yea, it idles great as a 4 cylinder, running on the drivers side only, plugs still in the passenger side just pulled the plug wires.

ill have to try the vacuum gauge and see what it says