[msimon785]

I think that 0.25" to 0.375" (3/8) ground clearance is ideal. That said, I have never built a WCD. Additionally, every game is different. For Breakaway, one might choose up to 1" of ground clearance, whereas for LogoMotion, 0.25" is more than enough. As to your second question, I believe you infer lowering the gearbox as opposed to raising it. Nonetheless, you can machine profiles out of, say, .25" 6061 designed after the mounted face of the gearbox.
Also, if you'd shoot me your CAD, I could take a look at it and provide some help with the frame design. I would love to do so. Based on the screenshot, I assume you are using SW?
Good Luck!