I remember having one heck of a time getting that right rear corner torsion back in place. I also had rotten wood about half way up both sides and the back. It was about 3 1/2 yrs ago when I fixed my Sun-Lite. I had some pics posted on here some where.
Sounds like you may have made the right side to long when you replaced the wood. Or you didn't get the bracket all the way into the torsion arm. Hard to tell with our seeing it. Like bobndot say's, pic would help.
I think I ended up putting the bracket on and using a large C-clamp to force the bracket into position. I remember having the BIL come over and help.