I have something like what you are doing in my Talon. Custom engine harness but I set it up similar to how the factory did as far as where it gets power for certain things, what goes through the MFI relay, etc. Power for the ECU itself and the MPI relay in both come directly from my ignition switch now. The ignition switch also switches on a painless 7 circuit fuse box to feed the WBO2, etc. Make sure the constant power wire goes to the battery before the cutoff switch or you'll lose your internal log if you shut the car off.
I had some voltage control problems along the way, so my current revision has the alternator voltage sensing wire tired in at the ignition switch so the ECU and all of the related components see full regulated voltage. Voltage at the battery ends up slightly higher which is good for things tied directly to it, like the MSD box.
There are a lot of ways to set this stuff up, and I keep improving my setup constantly after I think it's "done," so whatever you do, make sure it's easy to work on and modify so you can make changes later.
I moved the battery to the passenger seat area to make things ridiculously easy to work on, for example.
