After another failed attempt, I decided to make the background black and the modules white so there was plenty of toner to bond to the PCB, and I can extend and estimate where the border is. This worked much better, though there were still many holes. I’m not really sure what I’m doing different. I couldn’t find my old stash of glossy photo paper, so I tried Kodak paper for the first try (bad results). My friend suggested using a page from a magazine (about the same as the Kodak paper). The “good enough” result was using the updated image and magazine paper.
Using this extra information, I filled in some of the gaps with sharpie and headed out to the shop. I made corner holes for each module hole, and tried to cut the flats with a coping saw. While I finished a few that way, it was a painful and slow-going. Later, I used the dremel again with a carbide milling bit. This method went very quickly , though there was more wavering in the final cut. I cleaned each of the holes with sandpaper and enlarged them enough for the modules to have a mostly tight fit.
Once I finished making and refining the holes, I cleaned-off the toner. After the toner was all cleaned-off, I soldered the entire surface. It took forever, but I needed to make sure that it didn’t oxidize, preventing soldering later. With the entire surface “tinned” I put it in the toaster oven to smooth everything out.
While in the toaster, the bottom side of the board, which I’m not going to solder on, developed a pretty oxide layer. In the above photo, I have the master oscillator installed. I’m still not totally sure if it’s 100%, and I still need to solder on one more connection to it, but once those things are taken care of, I’ll solder on a cover.