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Ships operating F-35s--B or C models--require installation of some specialized electronics in a "classified" compartment. Without this, they're perfectly capable of handling the aircraft, but not "operating" it. F-35s have extensive data link ability, and this classified compartment permits full use of that feature. Ford was built somewhat concurrently with F-35C development, so the compartment was not added, but planned for "later." For "scheduling" reasons of some sort, it was also to be skipped until later for JFK. It was scheduled for Enterprise. When Congress found that out, they had a fit and mandated that JFK be fitted. It was "preposterous" that America's newest ship not be able to operate America's newest plane! Fine and dandy, but that blew the schedule. The ship is/has been fitted, but there's one more delay.

For the F-35B, vertical version, the jet blast is so hot that special deck coatings are required. The Marines and the Navy worked together to expedite both the "secret compartment" and the deck coating on the Amphibs. AFAIK, they can all now operate F-35B. If I'm not mistaken, they--at least initially--did not coat the entire flight decks. F-35Bs can/could only land and launch from specific treated parts of the deck. I have heard that the jet blast deflectors of the CTOL carriers also need this coating. For its carrier trials, it was launched and landed from ships not fitted out for its operation, so I am guessing those then at least got their blast deflectors coated.

Excepting Nimitz and Eisenhower, all carriers that have had an RCOH (Refuleing, Complex OverHaul) are equipped to operate the F-35C. Those still to receive RCOH will get the ability then. Ford will eventually also be "caught up," possibly in this current extensive maintenace period. JFK now can, and Enterprise was always scheduled for it.

One last tidbit... the old C-2 Greyhound could not carry replacement F-35 engines. They don't fit inside. The new CMV-22 Osprey can carry them. So, the RCOH carriers which were operating F-35s also had to have the CMV-22 available. If only Greyhounds were available, spare engines had to be dismantled and shipped in assemblies. At least one carrier...T. Roosevelt, I think...did that, and I think the delpoyment was brief. Obviously not ideal, and not widely practised. The C-2 is now fully retired from carrier use (though still some land based use remains) so "this little detail" is no longer in play.