SL Hitoyoshi and JR passes

Hi there
We (my husband and I) will be travelling to Japan for 3 weeks in May.

Our FIRST week will be spent in Tokyo, travelling down to Fukuoka (by Shinkansen), down to Ibusuki and then back to Kirishima with all sorts of stops on the way so fairly no-brainer to buy a Japan-wide Rail pass I assume.

Our THIRD week (8 days actually) will be spent travelling from Kumamoto via Nagasaki and then back to Takayama and Matsumoto to Tokyo, So again a Japan rail pass would cover all and would be worth getting.

On our middle 5 days we shall be spending 2 days in Kirishima then travelling to Kumamoto (hopefully on the SL Hitoyoshi), and renting a car for 3 days to visit Aso & Kurakawa.

Since a 21 day Japan pass is hardly any more (in cost) than 2 separate 7 day passes, we had assumed we would get a 21 day one. (Also this would cover our final trip from Matsumoto to Tokyo, which the second 7 day pass would not, so we would need to pay this separately if we got 2 passes.)

However we are a bit concerned about the SL Hitoyoshi trip. We know you have to book that promptly a month in advance but we will not be in Japan or have activated our passes by then. We found that owners of the JR Kyushu pass are catered for as they have started doing online reservations for the steam train as long as you have a JR Kyushu exchange voucher which gives you a password so you can reserve you seat without buying a ticket. However I asked them and they do not offer the service to people with Japan-wide rail passes.

The alternative seems to be the telephone reservation service but would they make us pay for a ticket as well as the reservation even if we have a Japan rail pass voucher? How do we assure them that we will have the Japan rail pass activated to cover that day? Also we are worried we could be in a phone queue as others are taking the seats online, and then miss out.

Thank you
Joce