I am no expert on the Kyushu sightseeing and limited express trains, unfortunately. I just don't get there very often. The ride that I enjoyed the most was between Kagoshima and Kumamoto using the Hayato no Kaze and Isaburo-Shinpei, and then a couple of years ago adding the Kawasemi-Yamasemi. (I never took the SL Hitoyoshi, although it's possible to include this as part of the series.) I took that ride once from south to north and once from north to south, the first time predating the introduction of the Kawasemi-Yamasemi. It was a nuisance to plan and set up, especially the last time when I included the Kawasemi-Yamasemi. Connections, layovers, and availability of tickets get pretty complicated, and the Hayato no Kaze doesn't run every day. But you don't have to worry about all that, with the Hisatsu Line being closed (too bad, but hopefully the line will be restored by the next time you go to Kyushu...). I'm glad you got a ticket on the Kawasemi-Yamasemi, though, as the train itself is a real kick. The route they are running it on right now is completely different and you won't get the splendid scenery and interesting details of the usual route, but I think it's well worth taking anyway. I expect you will have fun riding it.
I don't know anything about the "A Train" but it looks like fun. I considered it on my last trip but I just didn't have enough days there.
As I mentioned earlier, the Ibusuki no Tamatebako (Ibutama) is kind of fun. It is very touristy (although so is the Kawasemi-Yamasemi), but it isn't very long. If you take it, try to get one of the seats that face the ocean (the ones all in a row, and not the paired regular seats; I believe if you ask for "umigawa" they will know what you mean, although those seats sell out first). You probably don't want to take it unless you come up with plans for something to do out there (basically requiring buses), unless you really love train riding for itself, in which case I guess you could just do a round trip. I took the Nanohana train on that line one way last year (it is not really a sightseeing/tourist train but is nicely painted on the outside, and more importantly it stops less often than the regular local trains, which I wouldn't particularly recommend).
Basically any of the operational trains are worth considering, if you ask me. It sort of depends on where you are staying. I have done Nagasaki as a day trip from Fukuoka, and Beppu is also not a bad destination. (Many foreigners find Beppu "trashy" but I really enjoyed visiting some of the hells there, and also the place where they the cook food for you using an onsen facility is fun. My memory is bad this morning and I forgot the name. You pick out various food items and then they put it into a steamer. It's not haute cuisine, but the entertainment value is pretty high.) Anyway, just the plain limited express trains to places like those are an okay ride and you can have a nice excursion with them. With the Kyushu Shinkansen available "free" with the JR pass, there are so many options on that side of Kyushu. (I have never been to Miyazaki or Oita and don't know anything about that side of the island.) By the way, be prepared for the fact that the Kyushu Shinkansen itself is not all that great in terms of scenery (enormous number of tunnels). Its virtue is its speed, and of course it is very comfortable.
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