I am using the opposite approach.
For shims I only added what I needed to clear the mechanism as the gear swings. It rises above the frame of the retract during the cycle.
I'm using 1/8" 5 ply wood. Tim Evans suggested adding material to the bottom side of the retract rails, and I'll use 6X32 bolts with blind nuts.
The doors that I have definitely have some thickness to them so I figure the further away from the bottom wing skin with the landing gear the better. I can shim the doors with standoffs to bring them in line with the bottom airfoil.
Sparky