2002 Neon, no third gear & clunks into drive

I changed the radiator on my 2002 neon with an automatic transmission.
Shortly afterwards, I hit a speed bump & I noticed a dragging sound.
The main wiring harness had come loose & wires were broken.
It appears that when my car was in an accident two years ago, the harness partially broke & some of the wires were spliced together. When I hit the speed bump, some of the splice wires came apart.
Before I got a chance to fix it, I noticed that the speedo was erratic & the car had no third gear.

I crimped & repaired all of the damaged wires, but it still has no third gear.
No matter what I try, it won't kick into third. Plus, when i first put the car in gear, it clunks into drive a little harder than I remember.

It there a wire that perhaps I missed that would cause me to lose third gear?

Out of curiosity, what ATF fluid did you use?

It wasn't low. I didn't add any.

I'm not real familiar with the 2nd gen neons, do you have a 4-speed?

I've never paid much attention, but I beleive it's a 3 speed that's now a 2 speed. I can get to 45 - 50 mph in second gear and that's about it.