smelled a burning smell, while pulling into garage. knew something was burning so backed out of garage and ran inside to get a fire extinguisher. soon as i opened the hood there were flames. it definatley ran bad when reversing. 1999 with 83,000 miles nice truck was running perfect. so i replace the alternator, and the wires running to it as they were burnt. now it seems to be in limp mode. running on 4 cylinders or so. any advice? it fires right up, but has no power and shows no cel

 

You probably melted some plug wires or cracked one of the coil packs.

 

only visible wires melted, were the little ones to the alternator. Isnt there a limp mode in these trucks? it starts right up, but missing a few cylinders.

 

Yes, if it thinks it's overheated. That would be an issue with the CHT sender and its wiring. However, the CEL should be on.