Hi David,
I had wondered about the firmware and whether that was the issue - perhaps something I'll look into if it is possible to read out (though given that there is no window on this old device I assume it has a PROM and so can't be changed again). When I was going through my debugging stage I did notice that the VIA version of the 82C42 did have an AT and XT mode. I thought I checked my non-VIA device and it seemed like it was running in an AT-like mode (although now I can't remember if I was just checking whether the wiring was correct for that set up ... I believe there is also a command to query the current set up - that might be a better test regardless of what I think I've set it up for ... in case older devices only support XT mode).
I've upgraded my old PC to run with CF and USB-based floppy a while back (though just with commercially available adapters as they are 486-based) ... which is what made me eager to get at least the CF side of things running on the MECB. It's so much more convenient than old spinning disks (and much quieter). I didn't realise that XT's could support IDE - but that would definitely make life easier!
Apple II's are fun too - it's actually what got me into retro-computing again during COVID i.e. I purchased a non-working Apple II plus off e-bay (I never owned one when I was younger - we could never afford one) but had fond memories of it because we had plenty at school) and made it a project to get it running again (it had quite a bit broken including a problematic PSU, a couple of TTL devices, lots of 4116's on board and on the language card, some damage on the 80-column card, and the keyboard was flaky). I did finally get it up and running (my suspicion was that someone plugged in the ribbon cable from the language card the wrong way and it sent +12V and -5V into all the wrong places - I'm really not a fan of 4116's and had the same problem as yourself trying to source new working ones

). Are the serial / language cards your own design?
I have an Apple IIe and IIc now as well (the IIe has a super serial card and Z80 card running in it). I've also been playing with some more modern adaptations in these including the ESP32 soft card, a Raspberry Pi based Mouse card and a similar VGA output (which is really nice because the composite output is horrendous and I'm struggling to find any modern devices that work well with it). I'd be keen to try Fujinet on one of these as well at some point but have a few too many things all going on at once (I checked the IIc and it seems it does have the correct ROM version to support the Smartport so that is at least a good start, the IIe would need an extra card). Let me know if there is anything I can help with in regards to getting the Z80 card running (I'm not sure if it is similar to my one).
Cheers,
Emil.