I second what vtgtm said. The UHFB ('vette Under Hood Fuse Box) will still be used as that is what the engine harness connector plugs into and also interfaces with the ECU. The UHFB is already configured for the ECU to be able to operate the cooling fans, injectors, AC compressor, etc, etc. The only reasonable way to get rid of the UHFB would be to buy an aftermarket engine harness, which would come with a smaller fusebox already attached. The upside is that it would make the wiring much easier instead of all of the splicing and work-arounds needed with the UHFB, and it would cut about 5 pounds of weight by eliminating the UHFB and all of the bulky connectors that go along with it. The downside is that usually the aftermarket engine harnesses do not come with any of the AC circuits wired, so you would have to wire all of that stuff from scratch....and instead of having relays for low and high speed cooling fan operation (like you have with the UHFB), it will just have a single relay for cooling fan operation.....both fans are either on or off.
And yes, as far as the ISIS is concerned, pretty much all it does is provide an IGN ON circuit to the engine harness.....so whether you use the Painless and send that ign on signal from the key-switch, or use the ISIS to send the ign on signal from a Powercell, the engine harness does not care which.