I've recently got my AR3 integrated with ROS (more details here) and as part of the process had to shift the J2 and J5 encoders to read joint positions directly. I have a significant amount of backlash and slip in J2, J3 and J5. J3 is not as big an issue as it is calibrated under tension. However, getting more accurate joint position measurements for J2 and J5 was necessary for planning in MoveIt.
I've designed adapters for mounting the J2 and J5 encoders directly on the joints.
They are both designed to be added on with almost no disassembly required - just removing a few screws. The re-wiring of the encoder cables may be a little more tedious depending on how neat you want it to be. These were done up to the best of my very limited CAD skills, and I understand that Chris is also working on a proper design, but I hope that they will be useful for anyone who wants an interim solution.
Inductive Limit Switches
I'm done repositioning the J5 limit switch to calibrate directly against the J6 bearing cap, which should be more accurate than using the belt carrier. I also took the opportunity to try out an inductive sensor, which I thought would be easier to position for the calibration angle than the mechanical switches. Having inductive limit switches will also help avoid cases of damaged or bent limit switches. It seems to have worked well so I'll eventually redesign and replace the other limit switches as well.