burnt altenator again

i just recently had a new head installed with the works TC,WP,HG, Ect and a tune up the truck still wont idle correctly and after she starts and warms up and is driving she sometimes shuts off as she is moving and when u try to start it again it takes a while. it also doesnt go past 60mph like something holds it back. also when i bought it it had a burnt alternator i mean it even smell burnt so i hgot a new one i just got the truck back and it burnt it again even some of the wires look burn. has any one encounter these problems? my truck is a 94 toyota 2.4L 4cyl 4x4 5spd

It would take a major short somewhere to fry the alt. Did any of the fuseable links blow too? One or more should have gone first to protect the alt.

no havent found any looks like who ever had it before installed lights and may be an alarm shoot even the radio was installed wrong it has loose wires. also when the blinkers right or left are used the battery and brake signs flash together with the blinker dont know yet any ideas