The VIN will give you the engine code, production plant, and body style. After that, it is detective work. Original paint can normally be found on the trans tunnel, under the upper parts of the quarters, behind the jams, etc. Interior color can be found under the dash pad, and behind knobs, etc. As far as deluxe (pony) does the car "make sense" ie, door has factory cut holes for lights, upholstery on the interior quarters, all deluxe parts intact and aged, etc. Transmission again is "does it make sense?" IE correct tags on transmission and parts match, ie, no 1969 toploader with HURST shifter with a 1967 Bell housing, etc. Look for the neutral safety switch wiring on the cowl. Missing, better chance of standard, original looking: probably an automatic. As far as build date, based on the VIN, you can be a SCHEDULED build date to within a couple days, via the Marti books.
That covers most of the biggies.