If you are having binding issues at each end then you likely have misalignment as you stated. I just made the holes in my bearing holder biger to give some slop. I moved all the way to the edge then tightened the bolts and it seen to fix my problems.
As far as the twist in your table, it is going to be difficult to remove the skins and re-glue. Not sure how twisted your table is, but your best bet would be to surface your top or your spoil board. Does the machine sit flat on your table or stand? Does it wobble? You might also check your stand or table (whatever you have your 2006 sitting on) to ensure it is flat and level.