In my opinion the best way to approach such a problem is to do so systematically. Try to narrow down the probable causes to focus on the likely problem. The first thing I would do is try to determine whether the problem is inside or outside the radio. The best way to do that is to substitute a different radio; if the problem exists with a different radio in your shack, then the problem is most likely outside the radio. (It would also be possible that the two radios have the same problem, but that's unlikely.) The best second radio to use for troubleshooting would be an antenna analyzer, because if you were to transmit at full power with a typical 100 W HF transceiver when the SWR changed suddenly, the transceiver's finals could be damaged. An antenna analyzer transmits a tiny signal and monitors the SWR, and wouldn't be damaged if the SWR changed suddenly.
If you don't have an antenna analyzer or a second radio, then you might consider going to a meeting of your local ham club and asking for help. Most ham clubs have friendly folks who would be happy to assist, especially for a veteran. Such a ham club buddy could well be an experienced troubleshooter with an antenna analyzer who could help you zero in on the problem in no time.
So assuming that you have an antenna analyzer connected instead of your FT-990, try wiggling the coax and such while you monitor the SWR. Test both antennas and all your favorite bands. Ideally, try doing it on a windy day so the antennas get wiggled also.
If the problem happens when your radio is connected but not when the antenna analyzer is connected, then the fault is probably in your radio. If the problem happens when the antenna analyzer is connected, then the fault is probably elsewhere. In that case, see if the problem happens with just one antenna or the other. If it happens with both antennas, then the problem is probably in the coaxial cable, or a connector, the antenna switch, etc. Work systematically to figure out where the problem most likely is.
You mentioned that your problem is intermittent. Intermittent problems can be a real headache, because you sometimes have to wait a while for the problem to recur so you can troubleshoot. You say that the problem seems to happen some time after you tune up, but maybe that's just a coincidence; for example, maybe the problem goes away after the radio warms up a bit.
I think you'd be best off having someone help you locally, but you could always try asking more questions here, or in our "ham shack" chat room (might require more reputation to use, not sure), or some other internet forum. Good luck, and let us know how you make out in the comments to your question!