The PCM runs off the same circuit as the fuel pump. That is one way to reset the PCM by removing the fuel pump fuse. The PCM whine/noise is typical after shutting off the car.

 

Ah, ok not something I paid attention to when it was running correctly. Might be a stupid question but after replacing the fuse I now noticed that when turned to RUN the check engine light comes on and flashes 4 times. I've hooked up my OBD2 and it doesn't bring up any codes but its no giving the green light of nothings wrong either

 

Are you sure its not 1 flash pause, then 2 more? If so, that's your code 12 for the battery being disconnected within the last 50 key on cycles.

 

No its a definite 4 blinks and then a pause

 

Well there is no code 4, so I am not sure what that means.

 

Got a few minutes again without anyone needing anything from me and took a better look at the car. Blink pause 2 blinks and then 5 blinks repeating. got a video of it just in case.
http://youtu.be/Qzw0sWcu6-o

 

That would be a code 12 & 55. Code 12 is the battery disconnect within the last 50 key-on cycles. Code 55 is end of codes. You're good to go.

 

Ok so assuming that the computer isn't completely faulty and giving an all clear code when it is screwed up, I'm still looking at something being physically wrong (broken wire or faulty part like a bad fuel pump).

I was talking to a delivery guy the other day and he had mentioned that he had one where the cam sensor was doing.
Does anyone know if that on the same circuit?

 

What are the symptoms from your car? Drive it for about 30-40 miles and the pcm will trigger the code.

 

Would if I could, the issue is my fuel pump blows as soon as you try to start it. Lucked out last night with all the christmas rush being over I got a chance to get some serious time in on my car and my father was able to help me out.

Cleaned some contacts and was able to find a short on the fuel pump circuit. Unplugged the wires to the fuel pump and the short went away, so the issue is definitely the pump itself.
Got the tank drained, gonna be a day or so before I get another crack at it.