Finished re-soldering the protoboard tonight. It's not pretty and I need a new soldering iron tip, but it's done. I have to test for unexpected shorts, but I think it'll be fine. I posted some project pictures of the results.

I didn't do a full prototype; namely I skipped the 2x16 digital inputs on the far side of the board. I do have the SPI and I2C headers ready for the parts I bought. This should be more than enough for the time being.