So back story, bought the legacy used,replaced timing belt, gears, crank and cam poisoning sensors.car was finally running great. I could feel wires dangling down under dash when I drove. Climbed under dash saw two green connector plugged them in and started car. CEL came on flashing quickly. Turned off csr, disconnected green connecters restarted car and the idle had gone from incredible to incredibly rough. It nearly wanted to die a couple times. It almost sounds/feels like it was misfiring but not sure if that's it. Could really use some help.

those green connectors are only used for a type of troubleshooting procedure - leave them disconnected.

 

 

not sure what they have affected, kinda surprising.

 

but, you might try to reset the ecu with a scanner - or disconnect the battery for half an hour. maybe let the car re-learn from the base map. When you start it the first time after the reset, try not to touch the gas pedal - it may also crank kinda long.

Haven't ever had any running problems after connecting/disconnecting the green plugs.

 

Could just be coincidence. Could be a vacuum leak somewhere. Loose intake hose clamps, loose PCV/breather hoses connecting to the intake tube.

Could have fouled the spark plugs.

 

Could have jumped timing. Did you replace the tensioner piston?

If it happened right after connecting the wires and was fine before, unplug the battery for half an hour. I bought a car that had a bad speed sensor and iffy spark plugs, but ran ok. I reset the ECU with a scan tool and it ran like complete garbage until I unplugged the battery and let the ECU reset. Maybe something similar happened.

I had a '96 before, yes I would say unhook the battery even overnight (some 90's models had a TSB about making sure the battery is unhooked long enough for the ECU ram to actually clear and not have random garbage data in it). My '96 would learn 'bad habits' like this weird stumbling stuttering at idle that would go away and be perfect after a battery unhook but after a couple days it would relearn its bad habits (though it probably had one or more sensors or other issues that made it learn those bad habits).

I've had three things cause problems like that in the past. A dirty IACV, improperly adjusted TPS, and a dirty or failing MAF.

The symptoms usually boiled down to weird things like running fine for a few days then idling really wonky, or having no power over 80% throttle, or misfiring on one cylinder even though nothing was wrong with that cylinder and it would run fine after a reset... Sometimes it's hard to diagnose because the sensor isn't far enough out of range to actually throw a code, it just screws with the auto learned tune.