peter we - Negative. As already discussed here and elsewhere, previous Marine op cost estimates were based on Harrier stats. But, unlike the Harrier, the F-35B (1) lands/takes off quite normally in CTOL mode and (2) is easy to fly in STOVL mode, so STOVL will actually be done only aboard ship (small detachments, on not all deployments), when training for same, and on the Marines' once-per-war off-base operations (with cameras rolling). That's about ten per cent, or under 50 aircraft.
Should we have let that case drive so much of the JSF design? But... Marines! But... Guadalcanal! Too late now.
Engines & KB - I think the ski-jump aversion has to do with deck space. Once you add fixed-wing to the mix aboard the amphib, the last thing you want to do is give up even more helicopter spots.
Currently, the Navy, Marines and the shipbuilders are all scratching their heads about what to do with LHA-8 and subsequent ships. It appears to be agreed that the well deck has to come back, but replacing Harriers with F-35Bs, medium helos with V-22s and bringing on the bigger CH-53K places a strain on fuel capacity and other aviation spaces. Some years ago there was hope for a redesigned LHA-X, but after the Ford problems nobody wants to touch that with a ten foot pole.
So the result will be some sort of compromise that the operators will have to figure out as best they can.
Meanwhile, speaking of non-existent issues - even the brand-new America will have a restriction on F-35B operations:
SNA 2014: Heat From F-35, MV-22 Continue to Plague Big Deck Amphibs | USNI News