James,
The BK2 axles are definately the way to go for the X6. The extra droop made a noticeable difference.
The gear box definately takes some patience to build
Dremeling the top shaft is the way to go like you did. I lightly snug all the screws down and add a drop of blue loctite. I dont seem to have the same issue with screws coming that far through that it rubs the slipper plate though
I also changed to the Losi slipper (which is a straight swap) I like the feel of the Losi slipper much better. I used the slipper spring from an old Hydradrive I had, but I believe most people use the spring from the Losi gas truck slipper.
I run the Losi shocks, definately very easy to build and make operate smoothly.
The steering link from the servo to the bellcranks does have a bit of angle, but it is not a problem. I had to grind a little bit from the nose piece for my servo as well. Never had a problem with strength. Grind out the minimum, and you will be fine.
If you havent already, make sure you go on 2wdrc.com and check out the forum and the tech area for some great tips on set ups and mods.
I keep making changes and the car just keeps getting better and better. You just need to stick with it. I have had it on blue groove high bite tracks and loose blown out bumpy "fluff" tracks, and the car has served me well!