I worked some more on my IBM XT build. Figured out some of the jumpers on the I/O card I recently installed and got the Serial, Parallel & Game ports all working. All done by trial and error, since I couldn't find any documentation for the I/O card. Thankfully the Turbo XT BIOS is very helpful, listing all the available devices and their addresses at POST.
I never managed to get the Floppy drive (or Gotek) working with the I/O card, no jumper settings seem to make a difference so I had to put the old Floppy Controller back in instead. I'll come back to that issue at a later date. The Floppy Drive is at least functional, using the original drive taken out of my Atari ST.
I temporarily removed the MFM controller card and set about trying to make the 128MB CF card bootable. Figured out XTIDE seems to not like IBM PC DOS 3.30, either from CF card or from the Gotek so I had to install IBM DOS 5.00 on it instead.
So now the setup is practically perfect - when booting from the MFM HDD, the Primary partition of the CF card is invisible (it's a backup/clone of the MFM HDD, so this is perfect) and the rest of the Extended partitions appear correctly with the correct drive letters, keeping my .BAT files all pointing to the correct places. I can access all drives & partitions if I tell XTIDE to boot from D at startup, which will be good for backup & maintenance purposes.
The only thing I might do in the future, is reorganise the partitions making the Primary partition smaller to match the MFM HDD and moving the free space to the end of the drive for an additional partition.