My battery drained while replacing my head gaskets.

The heads are on but all my intake stuff and some accessories are in the back.

When I hook up the jumper cables the running lights come on and the horn blows. When I turn on the ignition the wipers start up.

I pulled the fuse for the horn and the wipers.

But I cant get my back window to roll down.
Actually none of the windows will roll down but the mirrors still work, but seem to be backwards.

What has grounded out causing my problems? or is something freaking out because its not plugged in?

95 v6 5speed 4x4 4runner

 

i would never apply ANY electrical to a vehicle that has any major parts dissassembled.. . . . .assume there is a designed electrical flow through ALL parts of the truck. you have dissrupted it

 

Hook up EVERYTHING first. Make sure you get all the grounds.
If you still have those problems, then start troubleshooting.

 

That is what I would normally do. But with the amount of hassel to get in the back it would be handy to roll the back glass down.

The weird part is that every thing worked before my battery drained. That is why I figured I grounded a hot wire.

I dont remember a body computer on these that could go haywire.

 

I don't think you have a body ECU.

It sounds more like a ground related to your fuse box isn't connected or something in the box is shorted.
I'm not super familiar with these, so I'm making a generalized guess.
I do know that if there's a problem, fix the known "broken" stuff first; in this case your unconnected harness [leaving the coolant temp sensor disconnected wouldn't cause this, but I can't see what you have disconnected], so.....