Transmission over temp/won’t start

I have one of those commanders that when it
rained, water pooled on the floor of the driver side.
It has been this was no matter the sealing of the
sunroof, windshield and replacement of windshield.
After it rained it would also make the electrical
panel show all kinds of signals. This would go on
and on. Occasionally it would say transmission over
temp. I would take it in but the readings would
never be something workable.
Two weeks ago it started saying “transmission over
temp” consistently. If I just start the car it would
run. If I stopped, I would not start again for a while.
Or a couple cranks. The summer changed to fall
and I noticed while this was still occurring, I didn’t
have any heat. The air that blew was cold but if I
turned the heat off, I’d get warmer air.
The other morning in 40 degrees, I stopped for gas
and it wouldn’t start. I cranked it a couple times
trying to turn it over and it started smoking. It
smelled like wires. Now it’s completely dead.