Neither of the connectors that plug into the fuse junction box were small enough to fit through the hole into the side compartment. I was, however, able to remove the individual terminals from the connector. By doing this, I was able to re-route the wires that were long enough without splicing the wire. There is a little spring tab on the bottom of each terminal that holds it into the connector. By inserting a thin, flat object (I used a small jewelers screwdriver) under the terminal from the front of the connector, I was able to release the tab and pull the terminal out of the connector.
Here is what the terminal looks like after it's been removed from the connector. The terminal on the right was one that I bought to see if it would fit in the connector; that way I would only have to make one splice on the wires that were short. Because of it's different shape, it would not fit into the connector. Anyway, on the wires that were long enough, I would pull the terminal out of the connector, route the wire into the side compartment, and then just plug the terminal back into the correct position on the connector. For the ones that were too short, I did the same splicing and lengthening process as I did on the ignitor wires. Again, I did these wires one at a time to avoid confusion.
Once the wires were all re-routed, I wrapped the harness with non-adhesive wire harness tape. The harness now runs in front of the seat support bracket.
I still have to cut the plastic, but once that's done, there will be nothing sticking out behind the seat support. I think that will make for some nice, clean lines on the back end of the bike. Right now, the boxes are just sitting in the side compartment, but I'm planning on mounting them in there a little cleaner. I'll post details when that happens.