973 actually posted a very good youtube video following through custom gearbox design
https://www.youtube.com/watch?v=GCjBx3TXB6Y
I think the actual gearbox bit starts around 19 mins in.
For my team, we usually like to have at least 2 or so pieces of round tube as standoffs somewhere in there (with symmetry if possible). Those tubes are usually inset into the .25" alum plates about .125" so they stay concentric with their bolts and nothing shifts around. I used to make the annoying mistake of jumping straight to weight cutouts way too early and having to redo them over and over again, so my general rule of thumb at this point is to not move on to weight cutouts until I'm 100% confident in the geometry and have had several mentors approve everything. 973 also posted a very insightful look into gearbox weight cutouts. Hope that helps!