I have found that if the screws are rubbing on the spur gear, they have been tightened too much. We never file or sand anything in the tranny and never have a problem with binding. We just tighten the screw until it just starts to bind and then back it of a hair. You do have to open up that one tight screw hole with a drill bit so that the screw just drops through. Smooth as silk. Of course, loctite is a must to hold the screw in place. We have never had one come loose.
X-Factory is working on a new 4 gear tranny that will be much better. They are really taking their time to try to get rid of the current issues.
We have been running the B4 rear axles with no droop limiters and no problems and we got one of the first X-6 kits. We are switching to BK2 rear shafts to allow for even more droop.
For shocks, we just switched over to Losi shocks for ease of rebuilding. AE shocks aren't that bad once you get used to them but the Losi are easier.
As far as the arms go, we had to shim our B4 arms when we were running that and we had to shim our X-Factory arms. Everything requires shimming.