My truck won't come out of park

My battery died and my factory car alarm went haywire disabling my truck. I hooked the charger up to give it a jump. I then smelled electrical so I immediately unhooked everything. I got a new battery and and put it in. I was able to disarm the alarm enough so the truck starts but now my power windows don't work and my truck won't come out of park so I can drive it. What do I do? Is it the alarm system doing this? And how do I disarm it completely?