the tranny is fine but the check engine light is on and at low speeds around 30 mph the truck has a weird vibration but at 60 its gone and when it happens i can put it in neutral and put the clutch in and it keeps doing it so idk

 

Output shaft - I.E. Tail Shaft? U-Joint could cause that too.
Check the code for the CEL.

 

how could that cause a vibration?

 

yep check the code. Sounds like though you forgot to plug something in when r&r.

Ujoint can cause a large vib.

 

Sorry to be off topic, but varsis, doesn't your sig need to be updated? lol

 

i had to use a diffrent yoke and a conversion joint to get the tranny in could that cause the driveshaft to be off balance?