Thanks for the positive feedback everyone! The beta testers have had no issues that I'm aware of.
Here's an update on the project for those interested.
The PCB is essentially completely redesigned. I improved it by adding screw terminals for both the link cable connector as well as the midi jacks. That's designed for people that don't want to keep their kits on the bare PCB and house it in some sort of case. I personally wouldn't do that, but there was plenty of room so why not? I added resistor values straight on the board for easier assembly. I added the 4.7k resistor from pin 7 of the 6n138 to ground that nitro2k01 suggests will improve performance when powering it with a gameboy. Speaking of that, I added the footprint for a GBA/GBC link port connector, so you can use a stock link cable without cutting it in half. And for fun, I changed the silkscreen color to blue to better match the arduino.
Now for the bugs. The only one I've found so far is that the serial in and serial out of the link port is swapped. A PCB modification is actually quite easy as the traces are clear and isolated, and thanks to the screw terminal holes you have an easy place to solder them to. Two small jumper wires are needed. Also, along with the link port it seems like the dual DMG/GBC link cable I have does have a wire going into the GBC side 5v line, but the 5v lines are not connected through the cable. I guess that actually makes sense. What this means is that you can't power the arduinoboy with a stock cable. Using the screw terminals still works, and modifying a cable might also be possible.
Pictures are worth a thousand words so here you go:
