I have a 2003 F150 5.4 with the 4r70w transmission. I had to rebuild the tranny last summer (clutches were shot). I thought it might be more job than I wanted to tackle, but I did ok. Only issue now is that it won't engage 2nd gear when it's in drive. It just revs up in 1st to about 3500 rpm, then skips right to 3rd. Same way on the downshift. It downshifts fine from 4-3, but when I really get on it, it jumps right down to 1. If I manually shift it to 2nd, it engages. I've done the electrical testing and verified that the pcm is commanding 2nd, but the transmission stays in 1st. I read somewhere that the valve body might be the culprit. Can anyone verify? I'll replace the valve body if I have to, I just want some more input before I spend that money.

 

It is unusual for all the clutches to be shot at one time,so what caused that? Did you clean the valves in the valve body?
Here again , if there was a lot of crap floating around in the trans, there is a good chance the 1-2 shift section is restricted .