Wiring Harness

okay i need to know what i should do about my wiring harness because i have a automatic transmission and just got it but found out that 3rd gear was missing and when i found out that my car rev to 8000 rpm and shut down the hole while that happen my engine realy fuse blew but i replace the engine fuse with another one and started to drive it so that i could get to work and back but when i was driving it after i replace the fuse i drove for around about a day or so and smelt somthing in my car smelt like somthing was burning look under the hood and my wiring harness was melting but i look at all the wires in the wiring harness and only found 2 wires they grounded out somewhere but i was wondering if i could just splice those 2 wires and put some new one. what should i do please help me.

You need to use an ohm meter and check all wires in the general area. Also put one end on the body and check if any wires are grounded. Any wires in a shielded cable have to be replaced with new wire in a shielded cable. Walmart has some new wiring connectors with a threaded clamp on each end which I like for computer wiring harness. Put silicon around the ends to keep out dust dirt and corrision. Fix up your harness. I have purchased a good quality one from a scrap yard used a terminal disconnect and replaced bad wires.
The big thing is take your time and not miss any wires. I had a friend do a Volvo who missed a couple of wires and it took me most of an afternoon finding the problem.