Bus or train best for Kyushu...?

We're about to travel Fukuoka -Nagasaki - Kumamoto - Yufuin -Beppu. We'd appreciate advice if bus or train (or combination) is a good way to do this route and if there are passes that are good to use? We will stay 2 days in the cities which can affect pass benefits like 3-day passes.

Harry I would use trains for those trips except maybe Nagasaki to Kumamoto. You could do that by train and ferry to avoid covering the same ground again. You can check the fares at http://www.hyperdia.com/cgi-english/hyperWeb.cgi and then look at the available passes to determine the best solution for your needs. Make sure you get to Aso.

The bus station at Tenjin was handy so went Fukuoka-Nagasaki today in a comfortable 2 hrs. on nonstop bus for Y2250 each.
The route Nagasaki-Kumamoto looks challenging if you go the shorter way through Shimabara - but we're tempted in spite of the changes required.....

........does anyone know if it's better to travel Kumamoto-Aso by bus or train please? Would the bus ride be travel sickness inducing for the sensitive wife?

One bus per day travels all the way from Kumamoto to the crater of Mount Aso, while the train only gets you as far as Aso Station, from where you have to take a bus to the crater. From that point of view, the bus can be more convenient:
http://www.japan-guide.com/e/e4552.html

My husband and me have been to Kyushyu two weeks ago and took a bus (tourist version, called Aso#1)between Kumamoto and Yufuin. There are at least two advantages of bus over train. #1: the bus takes you direct to ropeway station (the ropeway to Nakadate crater). Alternatively you should take a bus from Aso railway station (40 min. oneway, not so often to leave). #2: according to JNTO site and Lonely Planet the highway between Aso and Yufuin/Beppu is more scenic comparing with JR track. And it IS really scenic!
Ticket for Aso#1 route from Kumamoto to Yufuin is 5,800 yen per person including lunch on ropeway station (japanese one, was quite OK). The bus makes a 90-min. stop at ropeway lower station - it's quite enough to have lunch (10 min.) and get to crater (ropeway leaves to/from crater on 00, 15, 30, 45 min. of every hour, ticket is not included, but they give a discount for bus groups - 900 yen instead of 1,000 both ways). At Kumamoto you can get on the bus at JR station (at 10:00 AM) or at Bus Terminal (a few minutes past 10AM). The only tough thing (if you don't speak Japanese) about the bus is reservation: it's precondition for this route, and you can make it by phone only and in Japanese only.

Harry, me myself is very sensitive in this way. The bus trip between Aso and Yufuin definitely demands taking some medicine aganist travel sickness. But I'm not sure that is not a point for a train too: I became travel sick on LEX (limited express train) between Fukuoka and Nagasaki (!)

... was as follows: Nagasaki - Kumamoto by train (change in Tosu), Kumamoto - Yufuin by bus, Yufuin - Beppu by train (change on Oita). BTW the train from Yufuin to Oita is diesel engined, not electric one. :-)

Thanks so much for your help x3 Maria. Booked on the hwy.bus tomorrow,Nagasaki-Kumamoto, mainly because there's no change required enroute. It's raining steadily so we put off our plans to go via Shimabara with ferry and all.