Alright I still have this problem, I changed the solenoids still does the same thing. In Low gear it goes in to first, in 2nd it goes to 3rd and in D it goes to 4th. 1jz auto. Whats wrong with it?

Recap
L = 1st
2 = 3rd
D = 4th

How can I troubleshoot it?

 

not for nothing but i think your best bet is picking up a used 1j tranny and swapping it in there.

 

Kinda solved, it was the ecu not making it shift right. I still think I got a wiring problem too, the overdrive didn't work when I put in a ecu that I borrowed.