If you're using a different ignition switch, you can make things a little simpler by using the brown/black at the igniter to feed the 100Ω resistor/gray wire into the igniter's other pin (it doesn't have to run all the way to your ignition switch, since Br/Bk is already switched with the ignition).
The OEM "SH" R/R uses the brown wire to sense voltage in the system. The newer "FH" units get that off the main power wire. If you spend a few bucks to upgrade the R/R, you can eliminate the brown wire too (in addition to the standard upgrade benefits of more efficient and consistent output). The FH016 off an '07-'08 ZX6R has wire pigtails so you can install whatever connectors you want, rather than the molded
Furukawa connectors on most other FH models.
The white wire from the R/R doesn't need to go to the ignition switch. It may just be convenient for you to connect there, and that inherently routes it through the 30A main fuse. But you can wire it directly to the battery (with another fuse just to be safe). Or you could wire it directly to the main fuse connection on the starter solenoid. Same thing as now really, just the other end of that wire.
The current fan setup mimics the OEM wiring. The fan will run any time the sensor is hot enough, regardless of the position of the ignition switch. I wouldn't expect it to be an issue in any normal situation, but someone could drain your battery by holding a lighter on the sensor or something stupid like that. Some years of the EX500 had the fan circuit powered by the switched brown wire, so the fan will only run when the ignition is turned on. You may consider making this a switched circuit as well, rather than always-on.
The stock junction box has a "starter circuit relay" in it as well. The starter button flips the relay, which triggers the "starter relay" (solenoid) that actually powers the starter motor. I'm not sure how much the solenoid actually draws, but make sure your ignition switch can handle it if you're not using a relay.