I'd sand the fuselage to match the bulkhead. I had a Thrush at one time and I clearly remember that STRANGE L.G. mounting system. Actually, what I'd do, if you haven't glued the bulkhead in yet, is replace it with a thinner piece of wood, install a landing gear plate in the bottom of the fuselage, and use aluminum sheet landing gear held in with nylon bolts. I've just never liked the 5/32" wire L.G. system. Bends too easily.

Dr.1