And indeed the wiring job that dealership did was in-fact correct. I tried different combinations and they all ran rough at around 2800 RPMs. I think I'm at a loss guys but I did find this out. I got a good ODBII read yesterday and these are the codes that popped up..

P0121
P0122
P0306

After looking these codes up...

For P0121 - The Throttle position sensor is a potentiometer that measures the amount of throttle opening. As the throttle is opened, the reading (measured in volts) goes up. The powertrain control module (PCM) supplies a 5 Volt reference signal to the throttle position sensor (TPS) and usually a ground also. A general measurement is: at idle = .5 Volts; full throttle = 4.5 Volts. If the PCM detects that the throttle angle is greater or less than it should be for a specific RPM, it will set this code.

Potential Symptoms

Symptoms of a P0121 trouble code could include:

Malfunction Indicator Lamp (MIL) illumination (Check Engine Light or Service Engine Soon light)
Intermittent stumble on acceleration or deceleration
Blows black smoke on acceleration
No start
Causes

A code P0121 may mean that one or more of the following has happened:

TPS has intermittent open or short internally
Harness is rubbing and causing an open or short in the wiring
Bad connection at the TPS
Bad PCM (less likely)
Water or corrosion in connector or sensor


For P0122 - Throttle Position Sensor/Switch A Circuit Low Input

What does that mean?
A P0122 code means that the the car's computer has detected that the TPS (throttle position sensor) is reporting too low a voltage. On some vehicles that lower limit is 0.17 - 0.20 volts (V).

Did you adjust it when you installed it? If the signal value is less than .17V then the PCM sets this code. Could be an open or a short to ground in the signal circuit. Or you may have lost the 5Volt reference voltage.

Symptoms
Symptoms may include:
Rough or low idle
Stalling
Surging
No/little acceleration
other symptoms may also be present

Causes
A code P0122 may mean that one or more of the following has happened:

TPS not mounted securely
TPS circuit short to ground or another wire
Faulty TPS
Damaged computer (PCM)
Possible Solutions
Some recommended troubleshooting and repair steps are:

Carefully check the throttle position sensor (TPS), wiring connector, and wiring for breaks, etc. Repair or replace as necessary
Check the voltage at the TPS (refer to a service manual for your vehicle for specific information). If the voltage is too low that is indicative of a problem. Replace if necessary.
If recently replaced the TPS may need to be adjusted. On some vehicles the installation instructions call for the TPS to be properly aligned or adjusted, consult a repair manual for specifics.
If there are no symptoms at all, the problem may be intermittent and clearing the code may resolve the issue temporarily. If this is the case then you should definitely check the wiring to be sure it's not rubbing on anything, grounding, etc. The code may come back.


For P0306 - Cylinder #6 Misfire Detected

What does that mean?

A P0306 code means that the the car's computer has detected that one of the engine's cylinders is not firing properly. In this case it's cylinder #6.

Symptoms

Symptoms may include:
the engine may be harder to start
the engine may stumble / stumble, and/or hesitate
other symptoms may also be present
Causes

A code P0306 may mean that one or more of the following has happened:

Faulty spark plug or wire
Faulty coil (pack)
Faulty oxygen sensor(s)
Faulty fuel injector
Burned exhaust valve
Faulty catalytic converter(s)
Running out of fuel
Poor compression
Defective computer


Something else I also noticed..
My Pressure Sensor that sits on top of the manifold by the intake plenum is literally the only thing I didn't replace.. if that thing didn't work.. would it throw a code for MAP sensor? Or if it didn't work correctly, would it even throw a code or disrupt the IAC or Throttle Position Sensor?

I looked on amazon and found this.. it's exactly what I bought and replaced from autozone.. twice. Except autozone sells the duralast stuff, which in my opinion, is garbage. I saw a regular ACDelco TPS and a Professional ACDelco TPS (listed on the link below).


Just a heads up.. What I replaced already within the last 4 months to rule them out..
EGR Valve, IAC Valve, TPS Sensor, TPS Sensor Adapter (w/ wires), throttle body gasket, fuel pressure regulator, all hoses and vacuum lines and gas lines, air filter, cleaned out mass air flow sensor, cleaned out and scrubbed throttle body and plate.. I think that's it.

The dealership did say that the throttle body itself needed to be replaced because "it's getting old, it's tired". Can't see it. The throttle body itself, in my visual inspection looks just fine and the throttle plate itself is nice and flush. Spring is nice and tight..

Dunno.
Thanks guys.
-Johnnie