Your scheme sounds feasible but it can still be done as one compile project!!. The HOST PC utility that then supports re-programming van be used to separate the portion of the HEX file you want to download, loader bios or application.

I see little point of trying to make a PC architecture out of a microcontroller. You should concentrate on just making the loader simple so it can be FIXED and include yout I/O in the applications so the I/O can be made more special for each application. It turns out that the I/O functions are usually only a small part of the application code anyway.

Michael Karas