Is there any reason why you can't try the latest version 0098 BIOS for this board?
Even if that doesn't solve your problem, Is there any compelling reason why the parallel port needs to be in EPP mode on this PC (rather than ECP mode)? My understanding is that ECP offers better performance anyway. Sorry I can't contribute at the deep level you've raised as it's over my head/beyond my understading on the topic but I think trying the latest version of the boards BIOS would be a good start towards possibly getting what you want.
Just because it's not in the change log, this does not mean that changes haven't occurred in this field (either deliberately or as a side effect of other changes). If you have a nosey at page 20, Section 1.7 of the Tech Specs for this board you will find that ECP (as well as EPP) is supported by the motherboard. What specific hardware do you have that doesn't support this (as sometimes new drivers will incorporate additional support) and have you tried configuring the board for ECP support and seeing how it goes.
If it was my PC and a fully functioning printer port was my desired outcome, I'd be flashing that BIOS in a flash. For someone who's talking about port functioning at the depth you are, flashing an updated BIOS version (especially using the 'Express' method if you use Windows) would be comparatively very simple so your preference to leave the BIOS as-is surprises me.