The Phantom is a beautiful little ship and a fine model subject. I built one from a Model Shipways kit a few years ago. At that time MS was selling a version of it with a cast resin hull; frankly one reason I bought it was curiosity about how well that medium would work for a sailing ship. Verdict: they made some goofs (I don't understand why the planking seams on the deck are indicated and those of the external hull planking aren't, and the designer missed the "step" at the base of the bulwarks, and he forgot that the little cockpit in front of the steering wheel is supposed to be recessed a couple of feet below the surrounding deck), but the basic concept is sound. Apparently the kit didn't sell well in that format though. MS has now reverted to the machine-carved wood hull - just about like the version of the kit that was originally released back in the 1960s (but with Britannia metal castings this time, rather than the old lead alloy ones).
I probably won't be able to help much with this group project (though everything from the deck up on the resin-hull version is essentially identical), but if anybody's interested here are some photos of the finished product: http://www.hmsvictoryscalemodels.be/JohnTilleyPhantom/index.html
Regarding references - I don't think anybody has turned up any photos of the Phantom herself. The kit plans are by George Campbell, one of the very best, and contain just about everything you'll need to build a nice model. If you want to learn about American pilot schooners in general, here's a link to a book that's an excellent starting point: http://www.woodenboatstore.com/prodinfo.asp?number=325-122
It contains a contemporary painting of the Phantom and some really beautiful photographs of similar vessels. An expensive book but a beautiful, useful, and informative one. Highly recommended.
Another good source, though much older, is Howard I. Chapelle's American Sailing Craft. I contains quite a bit of information on pilot schooners. Chapelle, for the benefit of anybody who's new to the hobby, was one of the great historians of American naval architecture; he almost single-handedly created that field as a subject of scholarly study. That particular book, I believe, is out of print, but used copies are fairly easy to find on the web. Also highly recommended.
I have one significant quibble with the kit. A pilot schooner can't function without at least one small boat (in which one of the apprentices rows the pilot himself to and from the big ships he's piloting). For some odd reason the boats carried on board pilot schooners seem to have been called "canoes," though they didn't look like the canoe shape we usually think of. The kit doesn't contain one, and the plans don't mention it. I didn't bother adding one to my model, mainly because stowing it on the deck would mess up the lovely silhouette of the ship herself. But an authentic model of a pilot schooner really needs a boat.
Good luck. She makes a beautiful model.