You're weakening your frame by breaking the upper-inner flanges for gearbox clearance. Instead of two C-shaped pieces of metal, try flipping the upper flange of the inner sheet pieces in the opposite direction, creating an "S bend" on the piece. This allows you vertical room for gearbox clearance while keeping the top flange continuous, which is important for the strength of the chassis.
Example:
https://imgur.com/FPFNjkd