Upgrade to standard to green some trips?

If we book (that is assuming we can travel to Japan in July, which looks very unlikely) a standard class Japan Rail pass, can we upgrade to green class seats on some of the longer journeys (Tokyo to Takayama and Takayama to Kyoto). We may also go from Hiroshima to Fukuoka but that depends on the advice we are waiting for, about whether to take a chance of rain and wind and go to Amami Oshima, or whether we would be better to go to Fukuoka and get a ferry to Iki island. At least if the weather is bad, we could do something else in Fukuoka .

If you "upgrade", you will have to pay not only the green car surcharge but also the limited express fee (known as "seat fee" in Hyperdia), which is a considerable sum. In other words, the Japan Rail Pass would cover only the base fare in such a case.

For example, for the trip from Hiroshima to Fukuoka (Hakata Station), you would have to pay around 7500 yen (while the pass covers the base fare of 5170 yen).

I certainly wouldn't try to upgrade to green seats - simply prohibitively expensive, and I've never ever heard of someone complaining about the ordinary seats being unsatisfactory.
As for 'rain and wind', it's rather unclear what you mean. Nobody can predict the future weather, in fact for an island nation like Japan, the weather forecasts beyond 3 days can be quite unreliable. If you mean a typhoon; possible but unlikely.

I'm a big fan of the trip from Nagoya to Takayama in the wideview hida, and the green car is the front car so you get to look out the front past the driver which is nice. another good way to get there though is to go Tokyo to Matsumoto (check out castle) then train/bus to Kamikochi then on to Takayama. I would stay overnight at Kamikochi (Onsen Hotel would be my first choice but the other hotels there look nice as well), then go on to Takayama the next day.

I think you'd find the bus fares are a lot cheaper, but more to the point it is a super pretty journey through the mountains, and easy to organise (as I am not very good at those sorts of things). also you will be getting to see the wideview route on the way back from Takayama to Nagoya, so you wont be missing out on that.

Kamikochi is really nice to stay at overnight. If you are up early enough, there are usually monkeys playing around the hotel, but they retreat into the forest when the tourist buses arrive.