Well first, have you changed the transmission fluid lately? You may have a clogged filter and low on fluid. Or bad bands and need a rebuild transmission. Plugged heater core? Replace it. Water pump doesn't pump all the time? You may have air in the system and a bubble gets into the system Make sure you have a full coolant system. I am not sure what the transmission has to do with the overheating of the coolant. You may have a transmission cooler for the fluid, butr the engine coolant system and the transmission system are not connected. If you bypassed the cat convertor, you are getting bad signals to the engine and the timing is way off, that is why you are getting overheating. A couple of hundred bucks will fix that. Like TransAm77 said, you may consider looking at car payments instead of fixing this truck. Check the coolant levels first, and getting rid of the air pocket may help the transmission cooperate better.