Chief Delphi - pic: FRC 1716 Drivetrain 1

1. I would suggest keeping your shaft to only 2 bearings. If you add more you make the alignment of all 3 shafts extremely critical and it can cause issues.

2. Attaching the gearboxes by the flanges is fine based on the shape of the flange, but the plates will be easier to make if you just have a C-shaped plate which would make a standoff the prefered method of assembly.
Either way make sure you have accessability to get them on and off.

3. Hex shaft is CHEAP! You can get it for around $1/ft through McMaster. I find it pointless to buy less than 6ft at a time because of shipping charges.

In general it looks like a decent single speed setup. I would definitely cut more access/lightening holes in the frame members however. I would also use .120" sheets. .080" is really thin. I don't think your bearings would like that.