Electrical problem? - Not PATS (LONG)

I need help! Let me start from the beginning. I will try to include all relavent information. A few months ago I had to change my battery (original battery just got weak and died). After getting stranded because the car wouldn't crank, I got a jump and went to buy another battery. The problems seemed to have started after that... although it may very well not be realted to the battery issue at all. That may be totally a coincidence. Anyways, I think the first time what happened is I was driving on the interstate with the cruise control on a the car suddenly jerked and came off of the cruise control. It just happen for a split second so I just thought, maybe a mis fire and planned on checking the plugs, coils, etc. Well a few days later I go to start the car and it would crank all day long but not fire up. The 'THEFT' light on the dash blinked. I also heard a buzzing sound coming fro munder the hood. I tracked it down to a small box with a harness plugged into it in the front passenger fender. That first time I just figured it was maybe the security system fouling up on me because I had recently changed the battery. So I unpluged the negative terminal and tried to reset the system. Worked that time.

Well to make the long story a bit shorter, the jerks while driving became more frequent. It seems like the ignition cuts off for a second and the car tries to die (if it's in gear and moving, it fires right back up because the clutch is engaged). But last week I got stranded. That THEFT light was blinking and the car wouild crank but not fire up and that buzzing in the passenger, front fender was singing away.

I searched all the threads on here and came to the conclusion that it was my PATS key. I had only one key and it was an aftermarket key (STRATTEC). I bought the car about a year ago and they only gave me that one key. So I had to end up towing the car to Ford and they just made me two new keys this morning. Problem solved... well not really. Driving from the Ford dealer to work this morning I had one good "jerk" and it tried to stall when I pulled into my work parking lot. I heard that buzzing sound for a second but then it went away and the car would start up everytime with my new keys.

I'm at loss guys. The last thing I want is to turn Ford loose charging me all kids of diagnostic fees to track this problem down. Does anyone know what that "buzzing box" is in the front passenger fender? Any ideas are greatly appreciated.

Well Murphy's law kept me from going and spending $140. I started to check around the engine compartment for loose grounds and sure enough, one of the smaller wires that go into the negative terminal was loose (only two strands were connected). Must have happened when the new battery was installed (had new terminals put on as well). So far it looks like it solved the problem. For now anyway...