Car rental for a visit to Takachiho Gorge?

We will be in Kyushu in October. (This is part of a larger trip around Japan, but I have 6 days left to allocate, and I thought we would spend it in Kyushu.) I've become obsessed with the idea of visiting Takachiho Gorge - it looks stunning - however it looks difficult to get to with public transport, especially with a 4-year-old boy. A 3 hour bus ride each way would be insane.

Anyway, I was thinking of staying 2 nights in Nagasaki, 2 nights in Kumamoto, and 2 nights in Fukuoka. In Kumamoto we'd rent a car for a day trip to Takachiho Gorge.

Does this sound reasonable?
Any suggestions for a car rental place in Kumamoto?

I must admit that I'm a bit intimidated by the idea of renting a car in a small town. How likely will it be that at least the rental contract or possibly maybe a staff member will speak any English?

1. Kumamoto is not a small town. If you pass them your international driving permit and point at the car you want i do not see the issue. Better yet, reserve the vehicle online.

2. I took the bus from nobeoka. Winding through suburban, countryside, mountains, rivers and lakes. Scenic. Many small towns along the way. Some no more than 20 buildings! Wonder how the kids go the school or the adults work.

3. Takachiho gorge is pretty. But to say it is stunning is an overstatement. I would not even place it under beautiful. But it is good to escape to summer heat. To food there is fresh and shrine food is good (31dec-1jan). There are many other even more beautiful gorges/valleys 'round the world. Surely not worth the 3 hour bus ride to and fro.

4. Your 2 nights in each city sounds reasonable. Although, i figure a full day and a night in Fukuoka is sufficient. Is an onsen resort in anyway interesting to you? Beppy, Yufuin, and Kurokawa is in the vicinity. Give them some love.

If not a night at Aso area is good too. Ever heard of Takamori Yusui canal park. Really cool place. Outside a park, inside is an unused highway tunnel filled with water features and lights.
Also the sky road.
Seeing horses and cows.
The onsen hotels littered through the countryside.
Perfect for car rentalers like yourself.

5. If you do insist on visiting Takachiho gorge, then i recommend taking the night bus or drive after an exhausting day. So your kid will sleep in the back seat.

Renting a car to go to Takachiho makes a lot of sense - although using it within cities like Nagasaki really doesn't, since public transportation does a fine job, and there are many places within walking distance of each other. Takachiho is quite a nice place - and given how violent Aso eruptions and columnar jointing created it over 100,000 years ago, it is indeed stunning. If you want to think of the Grand Canyon as just a big hole in the ground also, you can, but aside from the scenic geography there's a shrine going back about 1800 years, and the Japanese people attach a lot of mythology to the place. Around the shrines are cedars going back over 8 centuries. The Yokagura Dance is also something special to watch.
Many people combine seeing Takachiho and Mt. Aso, although the crater area is still off limits. If you see Aso, you can add some flavor by going up to see Daikanbo for the great view, and the Nabegadaki waterfall close by.
Two nights in Nagasaki is pretty good. There is a lot to see in the city:
https://www.youtube.com/playlist?list=PL7LcPcmoSg-gbw2yXNLK92siHyNqSNx...
and the food is terrific. The chanpon are saraudon are great, and the castella while not the most delicious thing you'll ever eat is still tasting some history. Seeing Unzen and Shimabara is another possibility.
Fukuoka has some good shopping, parks, and historical temples and shrines. One of the best is Nanzoin, just 20 minutes by train from Hakata Stn:
https://www.youtube.com/watch?v=lT4VQFmHFyM
Nakasu is also very colourful and eating at a yatai there is quite an experience. If driving, the view from atop Aburayama is very nice, and visiting Nokonoshima is quite relaxing. Depending on your interests, you could spend a couple of good days there.
There is also Dazaifu and Yanagawa to explore if you like.
I'd say 2 nights in Kumamoto is too much of you are just referring to the city. Spending a night at Kurokawa would be a great idea though, and seeing the beautiful Suizenji Garden is also a great place to visit:
https://www.youtube.com/watch?v=K9xyXmU8U1g
You can also get some other good ideas at:
http://www.visitkyushu.org

Are there any suggestions for car rental companies to use to book a car?

Although I'm well able to point at a car and wave an international drivers licence, I'd rather book ahead of time (and be able to read the conditions in English).

I was only thinking of spending 2 nights in Kurokawa as it would be 2 nights on either side of a day spent with a rental car. There are so many potential places to visit my head is spinning, so I suspect this won't be our last trip to Kyushu.

If this is not your last trip to Kyushu why don't you get a Kyushu pass to see the northern Kyushu. Next time around when you have more Time you could get the full Kyushu pass to see southern Kyushu too.

Takachiho is in a secluded region. I do not recommend driving there unless mountain driving is something you are familiar with. I truly recommend taking the coach from nobeoka. Nobeoka itself is along the same line as Miyazaki and beppu and oita and usa and Fukuoka. So there's much to be seen. No rush and no worries. Safety first.

I looked into Nobeoka as the bus journey would be much shorter, however couldn't find any accommodation for the nights we'd be there.

Mountain driving isn't a problem, however I don't like the idea of renting a car if I cannot actually read the rental contract. I'd hoped to book a car ahead of time. We'll have JR passes but wanted for 1 day to rent a car. Too hard it seems.