[blam]

"My first question was... was there significant enough geological transformation to sink a civilization a half mile into the gulf over the last several thousand years? "

Yup. The end of the Ice Age.

My theory: During the Ice Age the Gulf Of Mexico became blocked off from the oceans of the world when they were 300-500ft lower than they are presently. During that time of blockage, the Gulf Of Mexico dried up to become a large lake and someone build a city on the coast of that lake.
Then the ice melt from the Ice Age caused the world's oceans to rise, the 'dam' was breached and the 'lake' became a gulf again and now we have a city 1/2 mile under water. This happened to the Black Sea (Noah's Flood?) and some say to the Mediterranean also. (Probably a lot of other places around the world too)

Here is a map of the world's oceans with the water level reduced by about 300ft. Now, Imagine that map with the water level reduced by 500ft. Interesting things begin to happen around Cuba, Bahamas and the Yuchatan.

[blam]

Here is the latest article of other submerged cities, Atlantis? It requires that the Mediterranean be blocked at Gilbraltar during the Ice Age too.

The Search For Atlantis 'Ends At Ayia Napa' (Cyprus)

[glock rocks]

Here is a map of the world's oceans with the water level reduced by about 300ft.

Looks like there could have been (if not a land bridge) some easy island hopping from the Yukutan to Cuba.

Uh oh. supper. back in a bit...

[Ogmios]

Interesting theory, and very likely, the more closely you look at it.

Will have to look into that more, but you may be closer to the mark then you think.