The junction box and ignitor each have two multi-pin terminals that plug into them. After I unwrapped the wiring harness, I found that a lot of the wires would be long enough to reach the side compartment. The small connector from the ignitor actually was able to be fed through the hole in the side compartment intact. The other connector was too big, so even the wires that were long enough had to be cut, routed through the hole, and then spliced back together. If a wire was too short, then I would cut it and splice a length of wire between the cuts so it could reach. I did one wire at a time to avoid confusion.
For the splices, I crimped insulated butt splices. Before I crimped the splices, I slid a chunk of heat shrink onto the wire. Since I was using the heat shrink, I probably could have gotten away with non-insulated butt splices. There wer'nt any in stock when I went shopping for parts, so I just grabbed the insulated ones.
Here you can see the heat shrink before and after the application of heat. I matched wire colors as best I could. On the wires that had a colored tracer, I just wrapped colored tape around the wire every few inches.