93EXaccord

Im working on a friends civic (90 lx auto sedan) and he just recently had the alt. changed, as he left the shop not even 1 min down the road his CEL came on.

i tired jumping the blue connector and it gave no codeon the dash board, so i pulled back the carpet and the ecu light is blinking 12 short blinks. i found this odd as everything i have read says that it should use a moris code system of long and short... so is this actually an EGR code or is something else wrong

RevengeCRX

That type of code system is normal for civics and crxs from 89-91 in the U.S. My old d16a6 ecu blinks between 1-20 times indicating either a faulty o2(1 blink), to electrical load problem(20 blinks).
I believe more complicated ecus that have more sensors and whatnot to control use the short blink and long blink code system(1 long blink, 2 short blinks-code 12), including ecus that run vtec engines.
Besides that, a code 12 does indicate EGR valve problem. I don't have alot of experience with 90 civic lx engines, but if it does have an EGR valve, it may be unplugged, or may just need to be cleaned. Worst case scenario, you'd have to replace it.

RedlineBoyzCRX

I have a 91 CRX with B16a1 Swap, And mine does the long and short blinks on it.