Ricknkin
I am in the process of covering my second CG Chipmunk. I built in wing flaps on both. I did not use the torque rods that came with the kit but bought Dubro aireron torque rods and cut/bent to fit.
The kit wants you to mount the flap servo on it's side in the center section using the plywood servo support. I did not install the plywood support and installed the wing flap servo upright. Just keep servo as low as you can so that it does not interfere with servos mounted in the fuselage tray.
Did you mount the bellcrank system and run the ailerons off of one servo? I built servo mounts in the wings to run each aileron with it's on servo.
I think that it might be best to just cut the aft center section out to install torque blocks using the same material you plan to use as your wing flaps.

By the way what do you plan to power your Chipmunk with?