This kind of thing was relatively common in the late '70's going into the '80's.
Nothing sinister going on, the owner of the GT500 probably wanted to make his Shelby run. So he had a 427 or a derivative installed and was happy as a clam. Sold the CJ motor and got some money back. No big deal.
When I was a teenager and into my 20's, here in SoCal there were a number of GT500's, Boss 429's, and other what we now call exotic muscle car bodies available without engines available for quite reasonable. Why the engines were missing could have any number of reasons, the most likely a resto or hop up project abandoned. The stolen engine scenario, certainly possible, is more of an urban legend.
At that time not many folks figured that Baby Boomers would be willing to spend stupid, I mean REALLY STUPID, money on these old cars.