I think you'll find it more challenging than working on a Classic, that's for sure. I've had my II for about a year and a half (started out pretty rough) and I succeeded in finding just about everything I needed. Between a very active community of passionate II enthusiasts (check out mustangii.net) and eBay, you'll find just about everything you could imagine, and if you're willing to pay even the most rare items.
Many, many maintenance and mechanical parts can still be sourced locally at the auto parts store, online at RockAuto or Amazon, etc. Body repair panels are available, as are fiberglass bumpers, and there are quite a number of small manufacturers stepping in to make parts where the big boys have neglected us. But to be honest my fabrication skills have improved quite a bit over the year making things fit that weren't supposed to.
In my opinion, where you might see a II project turn into a money-pit is if you're looking for a 100% proper restoration. Interior parts are especially hard to come by, so if you want a NOS dash pad and original seat-covers you'll be paying handsomely. If you don't mind a really nice dash-pad cover and installing some Fox seats then you'll be golden. I say a money-pit because the aftermarket value of a nicely restored II definitely isn't astronomical so you'd be unlikely to recoup that investment. Which is nice if you're in the market for a nicely restored II, and doesn't mean that much to someone who wants to keep the car forever anyways.
So the rumors you've heard are true, it's a lot different than restoring a classic where you can grab your Year One catalog and pretty much build a whole car from it (even buy a full unibody if you're so inclined). It's one that I highly recommend though, it's a small and tight-knit bunch of guys who love the ugly duckling of the Mustang world, so it's fun to be a part of it.
If you have some specific things you know you'll be missing, let us know and we can give you a few pointers on where to look.