since you're trying to get it as low as possible then i guess you don't intend to climb the ramp, any maybe even push other robots onto your ramp, well turning frame upside down helps in this, also you can make something like we did (not sure what it's called) to lower the frame even more. it requires some machining but nothing too difficult(just needs a drill press and bansaw)
here's a close-up pic (our clerance was less than 1/8 of an inch last year)
as for the flat surface for the gearboxes, i'm sure there are many different ways to mount them, maybe come L channel, or you cut the places you don't need(parts not supporting the wheels)