Spent some more time soldering the final handheld NES project. Just like in routing PCB traces, the majority of the time seems to be in getting the placement of the components just right. For this particular project it wasn't too bad. My main concern was just aligning the components so that they wouldn't hinder the connection between the FPGA board and the proto shield. I wired in a Parallax Propeller Mini board to save on space. Here's what the finished placement looks like:
I cut a small slot for the lcd cable to enter through the board and connect to the led driver. I ended up desoldering the screw terminals from the audio amp board in order to save room for the usb plug.
The only connections missing now are the speaker, sd card, and joypad buttons. The plan right now is to mount this to a larger board where i'll have a bit more room to work with.