The situation is really pretty dire. Even back when PocketPC devices were in their 'best case' period for hobbyist tinkering(ie. fairly current, available either new or nice and cheap used), the Linux ports were
rough.
The onboard flash was usually eccentric enough that you could only run Linux from CF or SD, some devices you still had to boot to WinCE every time and use a program that did some clever memory twiddling to kick the device over to Linux(something like the DOS Linux loaders that had their uses back in the day, though I'm not nearly qualified to discuss the details; but the concept and use were similar).
Peripheral support(especially graphics) was also generally atrocious, makes today's proprietary-blobs-for-one-antique-android-version mobile GPU situation look like some kind of Stallman Valhalla. With the right witchcraft, some models could at least display stuff on screen, some 'ran linux' in the sense that a linux kernel running on the device could be made to chat over the USB dock or a serial header; but not much else.
Since that time, the sites, documentation, writeups, tools, and projects have substantially rotted. With the hardware supply dwindling and Android devices cheap and common(or expensive and fairly classy, if you prefer) virtually all the developer, tinkerer, power-user, and other useful people have moved on. At best, you might still be able to dig up copies of files and docs that aren't just broken links; but that's about it.
WinCE software (while that has its own limitations, like being WinCE software) is actually likely to be markedly less painful. It's not exactly still on the market; but the value of used/new-old-stock/not-yet-linkrotted/etc. WinCE software is close to zero, so you can probably score some with sufficient scrounging. Plus, while MS certainly doesn't give a damn about supporting you anymore, 2005-2007 wasn't all that long ago, so you can probably get a full WinCE dev environment, exactly as MS would have recommended, with nothing more than a bit of piracy and an XP VM with USB passthrough.
Lest this all seem doom-and-gloom; I do have one useful recommendation:
Pocket Putty. Exactly what it sounds like. Everyone's favorite Windows SSH client; but for Pocket PC. There's also a
VNC Viewer. Never could find any X11.
At this point, pretty close to useless as standalone devices(and yes, the batteries are probably shot in any case, Li-ion is born to die); but between Putty and VNC you might actually be able to get some nice little 'dashboard' style display screens tethered to a more capable computer(possibly even use them as 'heads' for the routers, NASes, etc. that run Linux properly and have USB ports; but don't have graphics output: even something with no physical graphics hardware can, if it has the RAM, run xvnc, which would allow you to use a pocket PC with VNC client as a 'monitor'. Not something you'd want to do video playback on; but a nice little bandwidth graph, or some alerts or something? Sounds fun.
(Also, you mentioned SIRFStar III GPS units: you didn't say if those were built in, CF/SDIO expansion, or some proprietary 'cradle' thing: in any case
those are very, very, well supported by practically everything, common, reasonably well regarded, spit NEMA strings over something that looks like a serial port, sometimes 3.3v, sometimes 5v, sometimes actual RS-232, sometimes USBTTY. Assuming that you can crack them out of their packaging and get the pinout right before you fry something, you should be able to use SIRFStar IIIs with damned near anything, with at most a serial level converter or suitable USB/serial adapter. Even if you have to junk the Pocket PCs, those might be handy to have.)