I visited the Morgan for the first time in the summer of 1966. At that time - and for a long time after - she wore the white painted "ports" on her hull, and the full ship rig. Generations of visitors came to take it for granted that that was what she looked like. She sat in a bed of concrete, not actually "afloat." In 1966, at least in the summer time, she actually set a full suit of sails. (I remember sitting with my father watching the rigging crew, consisting of one full-time staff member and two apprentices, furl them at the end of the day.)
I think the Revell kit, which was originally released in 1968 (source - Dr. Thomas Graham's Revell Model Kits) is an accurate reproduction of what she looked like at that time. It probably was based on the plans drawn by Walter B. Channing, which for many years were regarded as the standard source about her.
Sometime after 1968 Mystic decided to change its approach to exhibiting the ship. I don't know just when this happened, but I think it probably was in either the late seventies or the early eighties. The concrete "berth" was demolished, and she was hauled out of the water for extensive restoration. The curators (I have this from one of the staff members, shortly after she went back on exhibition) decided that the best way to restore her was to "bring her back" to a configuration she had when a bunch of photographs of her were taken - I believe in the 1870s or 1880s. That meant, among other things, changing her to the barque rig and removing the painted ports. The latter apparently had been added for one of her movie appearances. It's been firmly established that she never carried them during her whaling career - though many other whalers certainly did.
There's an "updated" set of plans that show her as she looks now - i.e., as she looked when those old photos were taken. (Caveat - it's a pretty safe bet that when the current restoration is finished, she'll look different in some way. Researchers are always coming up with new information.) They're reproduced in the book Mystic Seaport Watercraft, which is available from the Seaport. (It contains lots and lots of plans - including those of the whaleboats she carries.) Using the dimensions on those drawings, it shouldn't be too difficult to convert the Revell kit to the barque rig - if that's what the modeler wants to do. On the other hand, if the kit is built out of the box (ship-rigged, but without the painted ports), the result should be a pretty accurate reproduction of what she looked like in the 1840s and 1850s.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.