Good to hear your problems fixed.

Wish mine was!!!!

Hello everyone,,  I know this is an old thread but I just put my 90 SE engine/trans back In the car after a clutch , timing belt, water pump etc. After reconnecting all the systems I did a test start and it immediately went to fast idle and sounded normal. As it throttled back, the idle it got lumpy and sounded almost like a cylinder wasn't firing. I pulled each spark plug wired off one at a time and each one affected the running so they all have spark. I have one 2 wire connector that doesn't seen to have a mate. Its part of the harness branch where the TPS connector and flywheel sensor are. Its a longer wire but does not go anywhere. This may be the problem so I'm wondering if anyone knows where this connector goes ?

@ScottyB, can you take a picture, that'll really help (and welcome to TLF!)

 

That may be a superfluous connector.  I'll guess at MAP sensor connections, or maybe NRV back to front.

Would be worth running Freescan on it in order to read the error codes 

Air intake temperature sensor on the chargecooler?

Depending on how rough it's running, it might just be the ECU relearning. If it's not too bad, I'd take her out for a spin and see if things clear when driven.

Here's a pic of the connector.. it looks to clean to be superfluous.

 

If the wire colors are Black/Brown and Yellow/Brown it is the CTS connector.

Update on the rough idle:  I discovered the O2 sensor connector had unclipped while moving the downpipe during teardown. That problem is solved but now have another issue. Since I never used the AC due to it never worked,  I decided not to reinstall the compressor and capped off the lines. Problem is now the cooling fans don't come. I'm wondering if I can jumper it out ?    

PS.. The coolant temp gauge is working.

Cheerz

The ECU and the Coolant temp. gauge both have their own temperature sensor.

For the gauge the sensor is on the forward part of the engine block (waterpump) and is a single wire connection.

The ECU uses a sensor on the right side of the engine block, under the inlet manifold and has a 2 wire connector.

The ECU controls the rad fans based (mainly) on the coolant temp.

 

If the loose wire has not been plugged into the coolant sensor under the intake manifold then the fans will never come on, and the engine will not run properly.