Transmission shifting issue, restarting the car solves the problem?

So, it sounds like the car is in limp mode; we should run the codes to see what's going on.

Here is a guide to help you:

https://www.2carpros.com/articles/checking-a-service-engine-soon-or-check-engine-light-on-or-flashing

Also check the transmission fluid level and clean the throttle body.

https://www.2carpros.com/articles/throttle-actuator-service

See if the fluid smells burnt. Check out the images (below). Let us know what happens and please upload pictures or videos of the problem.

Codes come back for crankshaft positioning sensor. Changed it, but no results. Changed the pigtail, and no results. Same codes as before.

These are the codes:
P0335
P0725
P1574

P0335 stands for “Crankshaft Position “A” Circuit Malfunction.
P0725 the transmission input speed sensor problem.
P1574 Code Vehicle Speed Sensor

So, these will affect the transmission shifting including the crank sensor circuit issue. Did these problems all come on at once? If so, you could have a bad PCM. I would remove the PCM and check for water damage or corrosion on the electrical terminals if none is present replace the PCM. You can get a rebuilt unit by searching Google or Ebay. Check out the images (below). Please let us know what happens.

Yes, they all came at the same time, but the second 2 codes are gone, I replaced the sensor on the transmission as it had some damage, and I unplugged the vehicle speed sensor by the intake and cleaned it. Now the crank positioning sensor p0335 is still on, I had a spare and replaced it but no change.

P0335 stands for Crankshaft Position A Circuit Malfunction. So, the wiring/connector is not making contact. Here is a guide to help with the test for the circuit and I have included the engine wiring diagrams in the images below to help with the test.

https://www.2carpros.com/articles/how-to-check-wiring

Check out the images (below). Please let us know what happens.

I had an O2 sensor plugged in where the crank sensor was supposed to be, haha I feel dumb.

It happens glad you got it fixed. Use 2CarPros anytime, we are here to help. Please tell a friend.