The main ones I use, in order of importance/use;
1. Osborne Factory Assembly Manuals. Year specific. Great visual reference for the basics of how most things go together. Body, Interior, Chassis and Electrical are mandatory, for me, the Weld and Sealant is nice but only needed if doing welding and you want factory info.
2. AMK Guide to Ford Fasteners - cross reference from the FAM part number to this to figure out what fasteners were originally used. Or to take an unknown from the "bucket-o-bolts" and figure out what it is...
3. Shop Manual - year specific
4. Cochran and Davis - 64 1/2 - 73 Restoration Guide
And lesser used, but OK references if you want a bigger library
5. For interior/upholstery Art Trantafellos' "Mustang Interior Restoration Guide 1964 1/2 - 1970
6. General items, not overly detailed (kinda like a Chilton's) Taylor and Wilson "Mustang Restoration Handbook" (covers 65-70)
For Ford Small block engines the bible is Bob Mannel's "Mustang & Ford Small Block V8 1962-1969"