Thanks for the advice and suggestions everyone, especially Dbldutch who I know has been doing amazing things with this design. Thankfully most of your suggestions are easy to implement with almost no increase to BOM cost. That's been the biggest driver here: right now my total BOM cost all-in is right at 100USD and I'd love to keep it right around there if possible.
I'll certainly look into adding individual regulators for every IC. I think I'll adjust the main reg to be a 12V-5V buck and have individual 3.3V linears powering everything directly. That way I don't have to worry too much about power dissipation with a 12V->3.3V linear conversion but I can still get relatively low-ripple 3.3V.
Filtering for the 1PPS, 5MHz, and 10MHz lines is easy. I'll also probably do a new revision of the board with the traces a lot further separated, and add some inline resistors and maybe even LPFs to the 5 and 10 meg lines. I'll definitely look into the PWM cleanup as well; I didn't thumb through all 25 pages before getting to work so there's definitely some useful tidbits here and there that I missed.
Likewise, temperature probes for the case and oven temps are also fairly easy to add in. A good idea for sure, I didn't even realize the code had provisions for temperature monitoring.
As some of you probably guessed, the OCXO I was going with originally was the McCoy OSC92-100B (also known as the Isotemp 134-12), but it seems as if this is less common on eBay than I thought (I bought the last one). I had originally intended to distribute out boards to some friends for them to build their own, but that requires them to be able to get ahold of oscillators for cheap.
I'm now looking at the RALTRON OX4114A-D3-1-10.000-3.3. It seems to have similar specs to the OSC92, is much smaller, and is available from Digikey for cheaper than I got the McCoy on eBay. whoops, that one has no electronic frequency adjustment. Also linked the wrong datasheet. Looks like the hunt continues!
At the end of the day, my goals for this project are two-fold: 1) a fun DIY project that will result in a useful piece of lab gear when everything's done, and 2) something to help my various used bits of test gear stay relatively in-spec. I'm definitely no "time nut" but I do a lot of RF projects and knowing I'm close enough to an accurate frequency is all I really need. My service monitor was last cal'd in 2002 so I'd imagine a good external reference will help things out.
Oh, and by popular demand the extraneous power switch has been removed in revision B: