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Hi,
I literally just got off the boat from Yakushima. Thoroughly enjoyed my four days there. And was in Takachiho just last week.
First, I don't seem to recall a beaches in Ambo itself, at least I didn't see one. It does have a harbor where jet foils dock.
There are a few nice white sand beaches (nothing super amazing, but not crowded and nice views) scattered around the island--Nagata on the Northwest (about 40 minutes east from Miyanoura) area has a beach that can be cordoned off to protect turtle hatching areas. Next door, fifteen minutes walk is Inaka-hama beach, which I found the best of the ones I went to--very few people at this time, wide, view of Iojima next door; there is also one at Kurio, Kuriohama. This is smaller and also a landing site for turtles in the summer. Kurio is on the southwest side of the island, probably 1.5 hrs from Ambo.
Staying in Ambo is a good way to access early buses to the Arakawa Jomon sugi trailhead. Otherwise, for example, if you've got your own wheels (which is most convenient), it almost doesn't matter where you stay, though Miyanoura or Ambo are more central to most sites. Driving makes life so much easier--most of the island is two lane roads (1 lane each direction) and relatively flat. There's not a lot of winding either. The major road signs (i.e location names) are in English too and you can get a few English maps of the towns at the information kiosk at Miyanoura ferry port--very useful.
Public transport is way less efficient, but doable (I used buses the whole time). The buses can be expensive--for example, from Miyanoura to Ambo will probably be around 1000Y, each way. There are one and two day passes (2000Y and 3000Y respectively) to use on the Yakushima Kotsu line. Matsubanda is another bus company with some connections, but the pass cannot be used on these buses.)
Miyanoura doesn't have a beach either, but there's more services, at least in terms of food and information and public transport, I've found. Besides Inakahama, there is a beach probably within 5-10 minutes drive north of Miyanoura that seems to be catering to families. A lot more people there (not a ton, though) and it looks like some scuba lessons going on there too.
As for the Jomon sugi hike, it was rainy the day I did it, but today seemed like it'd be totally clear. It's up a valley, so it's often under clouds, but not that hot, even in July. My guess for April, it'll be on the coolish, bring a spring jacket (and raincoat or something water proof).
If you like hiking, I'd recommend hiking up to Taikoiwa rock (you can find it on the Shiratani Unsuikyo brochure). This goes up Toji-toge pass, which is a bit more effort, but the trail passes through the moss forest famous in Princess Mononoke. And the view from the rock on a good day is damned impressive. You might as well do the rock and the genrin (virgin forest) return trail in a long day.
As for Nagasaki, you can connect from Kagoshima via the shinkansen (either the Tsubame or Sakura), which will take you to Shin-Tosu where you can connect to a limited express to Nagasaki.
If you want to stop in Takachiho, it'll take a bit more effort. On the JR pass you've got two approaches. You can take the shinkansen up to Kumamoto, where you can connect to a bus to Takachiho (3 hours ride), but there are only 2 buses that serve this route a day, though. Alternatively, you can take a limited express to Miyazaki (Kirishima), connect to another limited express (Nichirin) to Nobeoka, where there are up to 15 buses a day to Takachiho (1 hour-ish ride). Depending on the connections, they may both be similar in the time it takes to get to Takachiho. If you're slotting in Takachiho before Nagasaki, I'd leave Kagoshima early, choose the Miyazaki route, get into Takachiho early afternoon and relax for the night (and see the gorge and Yokagura (see below). Next day, check-out and see Imano Iwate shrine and catch the afternoon bus to Kumamoto, where you can either visit the castle or connect onwards to Nagasaki.
Within Takachiho, you'll find it hard to really fill in an entire day, but there's a few really interesting things to see. Amano Iwate shrine is 8Km from town center and is served by a few buses from Takachiho Miyako bus center. The gorge is on the west side of town within walking distance down a winding road. You can catch lunch (literally) at the gorge. There are a few somen nagashi restaurants, where you try to catch the noodles as they rush by you down a bamboo water chute. Afterwards you can hike or row the gorge. You'll probably be done with the gorge within 2 hours. At night, there is a yokagura dance performance for the tourists (500Y) at the shrine, where locals re-enact four stories surrounding Japanese mythology. If you book a hotel or ryokan, you can enjoy some resting time and dinner before catching the show at 8PM (arrive early, like 7:20 if you want good seats).
If you're on a budget, transport to Takachiho will cost you about 4000Y extra that's not covered by the JR pass. Add that to the expense of Yakushima (cheapest ferry is 7900Y round trip (hydrofoils cost almost double that); buses will probably run you at least 1500Y a day; rent a car will be way more than that), you might want to give it a miss. If you're not that interested in Japanese mythology, I'd also give it a miss--the gorge is nice, but there's not much else to do). Also, these locations, Takachiho and Yakushima are not the most English accessible, in terms of talking. You can pick up English brochures and maps, though which will be super useful.
Happy planning.
-mike
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