A bit of googling finds that SMC is "Standard Microsystems Corporation", apparently got renamed at one time to SMSC and finally to "Microchip".
The FDC37C654 is a Super-I/O chip with a floppy disk controller, hard disk controller, two serial ports, and a parallel port. The datasheet can be found e.g. here from this page (not sure how stable this link is).
Configuration pins are
80/81 PCF0/1 Parallel Port Configuration (disable, 3BCH, 378H, 278H)
24/23 SICF0/1 Primary Serial Port Configuration (disable, 3E8H, 2F8H, 3F8H)
91/93 S2CFO/1 Secondary Serial Port Configuration (disable, 2E8H, 3F8H, 2F8H)
83 IDECF IDE Configuration (disable, enable)
89 TDCCF Floppy Disk Controller (disable, enable)
I would assume these correspond to 8 of the 10 positions in the config header at the top. If you can read the printing around the config header (remove the bridges if necessary), that should probably identify which is which.
If there's nothing printed on the board, you could try tracing the connections, or trial and error (pick a setting, try to access serial port etc.)
Interrupt pins are:
38 PSPIRQ Source of Primary Serial Port Interrupt (IRQ3 or IRQ4)
37 SSPIRQ Source of Secondary Serial Port Interrupt (IRQ3 or IRQ4)
49 FINTR Floppy Interrupt
39 PINTR Parallel Port Interrupt
And I'd assume some of these are part of the IRQ header. I don't see any Harddisk IRQ pin. Possibly the Floppy Interrupt is both for Floppy and Harddisk? Or just labelled "IDE"?
The Harddisk/Floppy DMA is probably available at the DMA config block, but I don't understand the details.
After seeing the photo of the backside: The configuration block on the top routes the middle pins ("2" row) to the resistors directly below, and then from the resistors to the chip on the front side. This means the "1" and "3" row have a constant voltage, representing 0 and 1, and you can figure out which is which by following the traces on the front, if there's nothing else written on the PCB around the configuration block that's not visible in the first picture.
Once you've identified which pin the jumpers go to, the above table will give you the settings to enable and disable the various parts (disabling is two 0 bits).
As the standard serial port configuration is 3F8H and 2F8H, a first guess is that serial ports are enabled in this configuration (because motherboard serials very rare). So then the "1" row means 1, the "3" row means 0. Try moving all jumpers from the top to the bottom, see if the conflicts are gone.
This will also change the two additional jumpers that do not know what they are good for (and I cannot see the front side well enough to trace), so do this at your own risk.