Time for another progress report. After a lot of trial and error, I have reinstalled everything, and used my experience to know what to build from source, what can be trusted (at least for now) from the system's packages and tamed the network.
TL;DR: I have now got a reasonable working system, with critical apps and subsystems up to date, on top of a recent kernel (5.11.1) and all built with a recent GCC (10.2.0).
Firstly, the fsck vs clock issueThe system clock battery is wearing and fsck (equivalent of chkdsk) is very fussy about the write time, mount time, last check time being in the future or past, and forces a full filesystem check on boot, even if the filesystem is not tagged dirty. I bought a genuine modern(ish) Dallas type chip, but it's not as compatible a replacement as they claimed; the original is a genuine Dallas (not Maxim) DS1287A and while they are available in the UK, at around £45 including VAT ('sales tax' to you yanks

), think I'll pass. I have toyed with cutting open the case and hot-wiring the battery as it seems easy enough to do; I do run an electrical workshop for a living and the woodwork shop downstairs are only to happy to let me borrow their tools.
But in the end, I don't really need a real-time clock and the rest of the system settings are in an NVROM on the motherboard anyway. The config file option in fsck to ignore the time when deciding to do a full check has been ignored for years, a bug only fixed in a recent release of the filesystem tools; so I built e2fsprogs from source and it now works fine. It only needs to work until ntpd starts, after which the system clock (Linux clock, not the RTC clock) is updated from the internet. This also involved building a few other things, including coreutils, which for some reason totally escaped me in my list of critical things to update
Secondly, the Gnome Network ManagerOn the new kernel, this continually causes alignment traps (wonder what special sauce the EV4 kernel in Debian 5 for AXP was spreading on Network Manager

); after spending a day getting it and its crapton of dependencies either installed or built from source, despite I might add the several bugs in the autogen script, it no longer has an issue, but still has trouble getting a DHCP lease. Since the system dhcp client and it's CLI app have no such trouble and I don't expect to be carrying the server into a Starbucks to poseur with it on WiFi, I've reverted to the system package of network manager ... then disabled the bastard! Thank ${DEMON} the self-build Makefile for GNM includes an
uninstall target or I'd be really pissed off!
General stuffI have built openssl, curl and wget and installed the latest ca-certificates from the
sid repository (which they 'nicked' from Mozilla Firefox, LOL); so now I have working SSL & TLS. Most of the system apps were build against the ancient versions that came with the system, so I need to build each as required. The only thing I really want now for networking is a GUI web browser, but it is a nightmare finding one that's functional enough to be useful but doesn't have a ton of dependencies or a custom build system that was designed when sky-high on crack

The most promising one so far is NetSurf but even that has trouble building. It's not essential, so I've stopped for now, but may try again later.
Next stepsI need to build CMake, as most current Doom source ports depend on it. Perhaps git too, the one in the Lenny repo is as old as Moses and has issues. If I can avoid updating glibc I will, as that's always fraught with danger. After that, or maybe before, I really must try and port Nouveau to AXP. With an EV56 CPU, i.e. one that can do efficient BYTE/WORD/DWORD memory access, there's no theoretical reason why this couldn't be done, indeed for any architecture. I really would like at least Dr Frag's *ZDoom stuff running in accelerated mode on the GF 8400 GS, if not full-fat GZDoom itself.
But now, I need a break!