SO, I own an obd1 civic and iv'e swapped in an OBD2 b16. after trying to check my CEL I am a bit confused. my 93 civic ex has a blue connector with 2 holes in which i inserted a paperclip(into each prong) after doing that i turned the key and my cel blinks once very quickly and after that i get only long flashes with 3 second pauses afterwards. this goes on forever, i sat there for nearly 5mins and it wouldnt stop.

sequence:
short flash- LONG flash -pause-LONG flash- pause-LONG flash -pause...

I just wanted to know if im doing the test right. it might just be that i have a code 1000 but am not waiting long enough, but if anybody could shed some light i'd be greatly appreciated =]

 

From what you are describing it looks like you have 3 codes there., but there are not any single digit codes that can be represented by a single long flash. So, you are def reading it wrong.

Here is a how to to make sure you are doing it correctly and reading them correctly:
http://www.phearable.net/tech/mil/readcodes.html

Here is a list of codes:
http://www.phearable.net/tech/mil/troublecodes.html