Drill press, a couple of extra drills, Dremel and tools, some more wrenches of various sizes, vices, bench grinder, belt/disk sander (wood and aluminum don't agree with benchtop grinders in general). Probably some tape measures and a few more pairs of calipers. A couple of vices are good; if you're getting a drill press, get a 2-axis vice that you can mount to it and you get better accuracy. Oh, and right: Center punch (used with a hammer to make sure holes don't drift when you start drilling).
A good solid chop saw can probably do most of the functions of a miter saw and table saw (and to some extent a horizontal bandsaw); if you get one where the blade can slide in and out with respect to the pivot point, you get some limited table saw ability as well.
The larger tools like a lathe, mill, or 3-in-1 combo are going to be a little trickier to deal with. If you don't get a desktop/benchtop unit, you could be sacrificing a lot of floor space and you'll definitely need some funding or a donated unit and tools.
For storage, use the KOP totes, and get some similar ones. Label. Stick to what's on the labels. Use to store robot parts, motors, wheels, motion components, pneumatics, etc. Repeat with a multi-drawer toolbox, ideally rolling, with tools inside.
There is one tool that I don't see on your list that could be very useful, if light duty. That is a 3D printer. There are some desktop models in the $2K range; they build plastic parts. If you can do CAD, they can make life a lot easier on smaller parts--and they can do both round and squareish parts. The BeachBots put some parts made by one we got from
http://thefutureis3d.com/ on their robot last year, and those parts ain't failed yet. (Also note that this is something that could go into the classroom portion--it doesn't spit chips everywhere.)