I managed to add an USB connection. Yes it works!
So I had an idea, instead of adding an interface board, why not just run v-USB on the atmega128rfa1, we already have 16MHz crystal and nice 3.3V regulated power, so according to vUSB wiki we can go with possibly the easiest and cleanest solution, literally just needs 3 resistors and an USB socket, so that should be easy, right?
It actually is. I got the prototype working in one evening. And that's including all my crap soldering work, up to and including ripping off a pad off the board (luckily there was another pad available for that line).
I had a bit of dilemma over which pins to use, eventually settling on 25:SCL:INT0 and 26:SDA:INT1. It required removal of R41 (which is a 0 Ohm jumper connecting 26 to 52 for some reason) and R7 (which is a 4.7kOhm pull up on SCL). After my soldering struggles with the prototype, I searched for some easy trick and I spotted the reserved spot for "U5" chip has the following signals on the right hand side: [none] vcc gnd sda scl. Which is just perfect for this application! I figured I could just solder a 0.5mm pitch connector tape there and all my problems would be solved forever! I meticulously designed a little board with USB socket, the 3 resistors and a power switch(optional really). Etched it using a laser printer toner transfer method, it came out pretty nice, the parts soldered into place with almost no problem. And then... the connector tape turned out much harder to work with than expected, maybe I'm doing it wrong (I mean, I guess cutting it into ribbons and soldering straight onto the boards doesn't sound that clever in hindsight), but after a couple attempts, I had to carve out the gnd line from the tips to avoid the shorts. Never again! Okay maybe like once or twice, because I printed like 5 boards (with slightly different configurations), but once those are gone I'm redesigning!
The vUSB part is not yet integrated with the text editor, right now it's "just" HID keyboard Example, but the potential for exporting the text files out of the device is pretty obvious. An USB bootloader could also be nice but not a priority at this time.