Are you sure it's a Trailmaster 3.5 inch? If so, the tie rod ends do have to be cut to gain enough toe adjustment. If it's a camber problem, check the lower a-arm eccentric bolts, I have seen them mistakenly installed with the eccentric washer on one side flipped differently than the other, locking the camber adjustment. The full instructions for that kit are here http://www.trailmastersuspension.com/instructions/TP49_50.pdf if you want to re-check what you went through installing it if you didn't have them.
I had A lifted ifs truck back in the day, and I was pretty rough on it, but anyway mine started getting out of line all the time and I found out I had bent the frame and everytime I put it in 4wd it pulled it out of line.