Thats neat and tidy. :-)
I've had great success making things like that watertight with shrink tube and silicone, or good old hot glue. Both of them need a scaffold of some sort to stop them from separating where the Molex emerges, a silicone boot wont stay waterproof for long. I'd fill the back of the plug and round each end with hot glue and then shrink it up with clear tube and it should be watertight and visible, with workable buttons.
You might need to recess them a little so the shrink tube doesnt latch them on permanently, and trim up the glue with a knife to make it er, pretty ;-)

hmmmm, I'll try that out for my prototypes, and I'm wondering if there is a similar industrial process if I wanted to scale this up for the crowdfund rewards? I'll look into it :) thanks!

You're welcome :-)

Lol yeah, I'd think twice about a batch of a thousand too, but it isnt very labour intensive or fiddly. Waterproofing is as Rad said, challenging...

You can either seal out or repel water, silicone does not capillary so a seal doesnt have to be airtight to be watertight. Whereas hot glue must seal or the water will just wick under an edge. A detergent barrier prevents wicking there by breaking the surface tension but its temporary.

And if you used 'Capsense' buttons you could just pot it in a box with clear epoxy, no moving parts... You'll need an extra pin on your microcontroller for that tho.

I'm not aware of any processes but that doesnt mean there arent any. Good luck!

The trackball was unique, but I guess buttons are more practical. Making the USB plug water tight might be a challenge.

I'm still open to it in the future, I need to spend a little more time on it so that can be version 1.5 or 2 :)