As far as the main gear strut doors
go the real plane had the same issue,
they added "flaps" to the trailing edge of the strut doors to "lift" the gear up.

Good to know about the engine, I'm putting a peggy in mine to.

Well if countersinking did'nt work(which took care of the LG bolt clearance issues)
adding a 45 degree Spoiler strip to the trailing edge of the door may work (although its not scale)

This did work a friends lightning that had the same issue.


main wheel well doors.... move the aircylinders to the front wheel well wall, instead of having them mounted to the engine mount
as depicted in the instruction book, this gets them away from the engine(heat) and the gets the airlines away as well and puts them in a better position leverage wise.
credit for this goes to Scott Rowen