I recently completed an auto to manual trans swap on my 94 3.0 2WD Ranger. As a part of the swap I replaced the ECU with a reman unit from RockAuto. The good news is the trans part went well and works great. The bad news is I got the dreaded high/surging idle issue soon after the swap (less than 100 miles). So I searched and read the various threads and chased vacuum leaks, replaced the IAC and looked for bad connections and wiring. Somewhere during the process I said bad words and decided to just overhaul the entire fuel injection sensor network (I know I may have done myself more harm than good). New parts to date are All Vacuum and PCV lines, Vacuum caps where I removed the Auto trans kick down line and the cruise control system, Inlet Air Temp sensor, MAF, Water Temp (both), EGR vacuum, EGR Balance and EGR solenoid, Evap canister and solenoid, Idle Air Control. and TPS.

The problems,
1) The truck starts fine and idles at 900 RPM or so as long as the clutch is pushed in. If I let off the clutch in neutral the idle climbs to 2000-2500 RPM
2) Acceleration is ok until about 2200 RPM and then lags like its choking until about 3500 RPM and then the engine opens up like an old fashioned carb on kick down
3) The CEL comes on intermittently, usually under heavy load like going up a hill or using the AC
4) I pulled the codes and get (KOEO) 118 Engine Coolant Temp Sensor above max voltage, 113 Intake Air Temperature Sensor above max voltage, 121 Closed throttle voltage higher or lower than expected, and 123 TPS above maxi voltage. And for Continuous Memory codes 118, 113, and 123 repeat.

I pulled the connectors for these sensors and cleaned them and inspected the wiring. No issues found. So my questions are,
1) Can these codes cause the drivability issues I'm seeing?
2) Did I just get bad parts for the IAT, TPS and Coolant sensors?
3) Can the ECU be bad?
4) Any other ideas?

Thanks