MSOCS - A Rover-type capability is supposedly a candidate for 4A/4B, but so far that list has not been finalized, as far as I know. Not sure about IR marker. However, it has been argued in this thread (and is missing from the latest Majumdar story) that any day video, including HDTV, is not possible.
As for upgrade costs: the concern has to be that the F-35 will resemble its cousin, the F-22, which has incurred annual R&D-alone bills that are the thick end of $1 billion since it entered service for rather modest capability upgrades and a lot of obsolescence fixes.
The idea that the F-35 will be easier to upgrade than older aircraft remains unproven. On the upside, the F-35 has more modern computers and is Ada-free. On the downside, any new apertures will have to be specially designed and the aircraft is limited in space, surface real estate, and cooling.
Hempy - The DN piece is interesting. However, it's notable that when a USAF guy talks "4th" vs. "5th" he's talking "USAF 4th". That is, F-15s with the rather decrepit, way-pre-DRFM TEWS, F-16s still stuck with RWR and no active ECM other than pods, no IRST anywhere, no intraflight datalink and 1980s glass cockpits. So, yes, F-22/35 are another order of capability. But USAF-4th isn't Rafale, Typhoon or Gripen, even today.