I use similar a similar squaring tool. I put in the bar square it up then use repetier to move it out and back to 0,0. My 0,0 is where the squaring tool holds it.
As for raising the material… I shortened my legs by 3 inches to 5.5 inches from 8.5. That makes a substantial difference in even just the rigidity of the frame. I decided I will most likely not be doing any printing on this big beast