Bret,
The fuselage kit build starts with the firewall. The instructions don't mention lots of the little things that eventually go on the firewall. You should definitely order the firewall forward doc set of drawings and add what you can while you are building the firewall. Even better if you know now what your engine will require on there. There are a couple of nutplates that need to be added for the fuel/oil pressure sender lines and breather tube. Also doublers for the electrical contactors, gasolator/fuel lines and battery box holes. Nothing too hard to do later, but it is a pain to have to go back and undo work. The top of the firewall also should be slightly bent forward to match the subpanel forward ribs. Much easier to get that crease done crisply before all of the supporting angles get riveted on.
As for other mods, there are an infinite number of ways to customize, but I can't think of anything you would really need to plan in advance. Conduit for wire runs, ADAHAR's mount, ELT mount, and servos for Autopilot are all extras in the fuselage build.