Hondata

1) Can you toss the adapter harness and plug the KPro'd ecu directly into an '04 if you set options correctly in software?

Or to put it another way, is the adapter harness the only hardware difference or has the ecu hardware been modified in some way so it can't function in a '02-'04?

2) Conversely, when you take a "05-'06 back to stock, can you leave the '02-'04 o2 sensor and Hondata adapter cable installed and run a stock PRB ecu? (Pretty sure this won't work but maybe I'm seeing problems that don't exist)

No and no. Once modified it will only work in an 05-06 and you cannot swap things back and forth.

What exactly is modified in the K-Pro?

It is something to do with the fact that the 02-04 RSX has VTC+ and VTC- while the 05-06 only has a VTC pin and used body ground for the negative for VTC?

I don't know all of them, but there are also changes made to the speed sensor circuitry to allow the high frequency sensor/dash gauges to work with the low frequency ECU. When I originally got my k-pro (2006) I was sent an unmodified ECU, even with the harness it wouldn't show the vehicle speed, wouldn't datalog and had a constant CEL. same would work the other way, it just won't do it.