Hello David,
Welcome back to the future!
The M3501 is a god keyboard with a firm feel, and if it quits working, you can always use it as a hammer to pound nails. The M2980 - if you can find a newer one without the Pepsi and Nacho crumbs - has a slightly lighter feel. Also, I just ran across an old Macally - my first; it's ugly as sin, but it works well and has a nice feel to it, too.
The best - by far - mouse I have found is a brand new Macally - still available, and usually for cheap.
I use eBay as a source for almost all my old Mac parts, and as long as I keep my eyes open and remember it's a flea market it seems to treat me well. Besides, there are literally thousands of old Mac pieces to be found.
If you perform a clean install/reinstall (sometimes called an "archive-and-install") with the USB card firmly seated in its slot, I think you'll find you can install any made-for-Mac USB card you can find. The trouble one usually has is that the Mac OS does not install drivers unless it "sees" the need; if the USB card isn't there, the installer doesn't sees the need and doesn't install. Further, downloading the drivers doesn't dislodge the AppleTalk protocol which tends to control unused ports - and that leaves you talking to yourself and saying uncomplimentary things about Steve Jobs. You can install the drivers by doing a custom install, or by using the Tome Viewer utility, but - all things considered - it's easier just to do a fresh install.
My own preference runs to the Orange Micro USB/Firewire card, but I've used at least a half dozen different USB cards and they all work.
FWIW, I use a Macally mouse and M2980 keyboard - even on my everyday Digital Audio, which requires the Griffin adapter. I think it's the soft touch that gets me.
You don't say what your project requires, but I can't help thinking I'd be looking at a 450 or 500mhz processor to make the day go a little faster, maybe even overclocking one step if you're not doing anything processor intensive. Those old ZIF CPUs are downright cheap on eBay these days.
Not so cheap is the combination of ATA-133 controller card and ATA-133 HD, but it really makes the old beige G3s bounce along.
It's enough to make an old Mac addict nostalgic!
Regards ..... Jon