I started my car this morning and left to go for a drive, like I always do on the weekend, I got a few blocks away and it smelled like something was burning, so I turned around and went home and found a fuse holder melting down and the wire burning in the trunk next to my battery. The fuse holder and wire connects to the alternator. I didn't find any issues with the wire, etc. so I replaced the fuse holder and tested it, all seemed to be okay. I think maybe the screw that held the fuse holder to the wall rubbed through the insulation and grounded out the wire. Afterward I left again to go on that ride I started earlier, all seemed fine. Then on my way back home I did a real short 3rd gear pull, maybe for 2 seconds max, and again all seemed fine but a few seconds later when I went to give it more throttle it was acting like a plug was fuel soaked. I continued to drive it easy, I've had this happen before and it normally cleans out and is normal again after a minute or so of driving, but not today. Got home and pulled the DTC's (no CEL though) found P0689 - Electronic Control Module Power Relay Sense Circuit Low, P0830 - Clutch Pedal Switch A and P0833 - Clutch Pedal Switch B. Well my car was originally an automatic, and still is, although the ECU thinks it's a stick since I have a 4r70w with MVB. So the motor runs okay but when you get into the throttle it starts breaking up, once I tried to stay in it to see if it would clear up and it leaned out and my LPM cut it off, that procduced another code P0171 bank 1 lean. I checked all the grounds, swapped PCM relays with no luck, any suggestions? I also checked all the plugs and they all look fine. I'm stumped with this at the moment, I don't know if that wire melting issue from earlier is related or not.