How long does it take the ECU after being reset to re-learn whatever it has?
I pulled the ecu on my 350TPI to check it was working fine, and at the same time changed the SES bulb, plugged it all back in and got code 12 when running shorted diagnostic pins.
Turned the car off, removed wire and started it and left it for 5 mins, and turned it off. That was yesterday, and then today I went for a drive down the road, only about a mile or two, and the throttle repsonse sucked ***. The car drove like a had a caravan in tow.
Is this because the ECU needs to take more readings etc? or is the problem elsewhere?

make sure all the connectors in the plugs are in foward in the connector. Sometime when you plug them back into the ecu 1 pushes back and the pins don't make contact. how was it running before you pulled the ecu? they relearn quickly, it would help if you list what kind of car you have on your profile also. check the pins 1 by 1

sorry bout that.
1985 Pontiac TransAM, with 290hp 350 crate motor, 87TPI setup, 16198259(re-man 165) ECU, 19lbs injectors, MEMCAL chip, extractors into 2 cats into a 3" exhaust system, stage 2 shift kit.
Pretty sure everything plugged ok, it was just running sluggish.

also if one of the pins didnt go through, wouldnt it come up as a code in the diagnostics?

IT SHOULD, BUT??? CHECK IT IF IT RAN GOOD BEFORE YOU TOOK IT OUT. MAKE SURE ALL GROUNDS ARE GOOD,

Nah it was running rough at idle, but it had a lot more power than there is now.
It was still nowhere near where it should've been for a 290hp motor but now it feels like I've got a caravan in tow.

maybe the cats are clogged

It honestly sounds like you are running a 305 chip with the 19# 305 injectors. If that is the case, your ECM is adding fuel and stores the fuel trims it last used. Driving it a good 30-50 miles will let it adapt and bring you back your power.

Thanks mate. I've got it booked in for a dyno tune thursday so they should be able to get it running good I'm hoping, or at least tell me whats wrong with it.

How can i tell if the cats are clogged and how can i unclog them?