In bios the port remains EPP, you do not need to change that. To change the mode you just have to add that to the HAL file at the part where it loads the parallel port driver, something like:
loadrt paraport "0x387 out" for normal operation, 8+4 out/5 in
loadrt paraport "0x387 in" for 13 in and 4 out
loadrt paraport "0x387 x" for 9in and 8 out
You have to double check that as it has been quite some time since i messed with that.
You can also add another pci or pci-ex card with parallel port so you can double the in/out pins as you like.
Then again, a Mesa 5i25 or 6i25 has two such ports and can operate at a much higher speed for a bit more money, worth every dime. I have nearly 4000$ of mesa boards installed on several machines, one 5i25 is still sitting in the box but not for long and a complete set consisting of 6i25, 7i77, 7i74, 2x 7i84 and a THCAD on a piece of wood with a PC wired and used for testing and making PyVCP panels as needed for machines i retrofit.