Why is my truck running "rough" and a lack of power?

I drove my truck home from work on Friday and everything was fine. Today I started the truck and it sounded and felt like it was running a little rougher than usual. I peeked under the hood and there was a mouse nest between the head and the manifold. When I finished pulling all of the nest out, I found a connector and the wires had been stripped. So I separated the two wires that run into the connection and they were not broken just stripped. I thought that maybe it was because of the 30 degree weather and the motor just needed to warm up. Well about fifteen minutes later I drove away and I found out that there was not much power. It will not accelerate very fast at all and when I go up an incline it decelerates. When I get to a speed where the transmission is going to shift, it gains the power back (about 5mph before and 5mph after shifting). What is wrong with my 1996 V6 Dodge Dakota?