I'm amazed at the amount of stuff I now treat as common enough knowledge in my life that I simply did not know upon arrival.
Like that the main station of Kobe is Sannomiya station, not Kobe station, although there IS a Kobe station, it probably isn't where you want to get off the train (unless you're going to Motomachi I guess)...
And I've gotten to a place in my life where I just kind of know how to get to the helpful information I want to use by either google searching key words in Japanese or linking through a series of steps that are natural to me. But it's high time I gathered these transportation links into one place for easier access (both for my own benefit, and anyone preparing to or continuing to live in Shiso).
Searching up directions to Shiso on a google map will give you some alarming results, based mostly on our lack of trains. It'll say something like, train as far as Shingu, then walk forever to get to Shiso.
But around here, the word to know is Shinki Bus, and that sucker will get you most places that you need to go. Unfortunately, their website is still Japanese only, but if you can operate in Japanese (or make your way though a google translate version), you are good to go.
Most especially the navi feature, which like hyperdia does for trains, allows you to put in your departure and arrival locations to search bus times. It'll give you several of the upcoming buses as well as the cost of travel. I have used this basically just to figure out bus times from Himeji to Yamasaki and back, but I'm sure it can be even more useful than that so long as you know the name of the bus stops you want to use. This is a local bus so it doesn't have luggage space underneath like the highway buses do.
Then, there are the highway buses, most often used by me being the Osaka and Kyoto buses. The line goes from Tsuyama to Osaka and Kyoto but their uses are different.
The Osaka bus is way more frequent any way easier to use. It goes by almost every half hour or so, and to get on you just.. get on. Take a little ticket showing that you got on at stop like 9 or so, and keep it til you get to the end. The bus terminates at Osaka station, but pro tip if you are going down to Namba or Shinsaibashi areas, it's easier and a tiny bit cheaper (not enough to really matter.. the best thing about doing it this way is more the avoiding of the massive entity that is Osaka Station City) to get off at Shin-Osaka rather than Osaka Station and take the red line subway downtown. On this bus it usually takes about two hours to get to Osaka.
The Kyoto bus only runs four times a day in each direction, and you have to buy the tickets in advance (I've gotten away without doing so, but it always seemed like a big deal to the driver). The easiest way I've found to do this is to roll up to Lawson and use the machine, because reserving online and then paying for them seemed to be a bitch. If you do this, though, you have to select the bus line first, so make sure you say you are going from Tsuyama (which is in the Chugoku region, not Kansai!) to Kyoto first, then later you can specify that you are getting on the bus in Yamasaki. The machines can be a little confusing and I mostly navigate it as I go each time on sight.
There is also a Tottori bus, which runs from Himeji to Tottori with a stop at Yamasaki inter. I don't know anything about this other than that it exists and some people I know have taken it before.
After that, there is the fairly new but apparently popular direct bus from Yamasaki to Kobe's Sannomiya Station, affectionately known to us as just "the Kobe bus." Unlike the other highway buses, this one leaves directly from the in town bus station, so you don't have to meet it at the highway gate unless you want to.
If you are driving, and planning to take the highway, and want to know how much that will cost you, check out this page, which can help you figure out your toll cost based on where you are going and what type of car you drive.
Flying? There are a bunch of small airports in the area, but I've only ever used Kobe, Itami, and of course KIX (kankuu) myself. I've heard good things about Okayama, and I know Tajima has an airport, but I don't know what it's used for. There is no longer a direct bus along the Tsuyama-KIX line, sadly, but from Himeji station you can get buses to both Itami and KIX. Kobe airport is accesses by the Port Liner, which runs from Sannomiya, which you can get to by direct bus.
Domestic flying in Japan is a breeze compared to doing it in the US, especially out of one of the smaller airports. There is security and paperwork, but it's nothing like the clusterfuck I'd learned to expect from flying. You can even bring your water bottle so long as you let them open it and check the contents (by machine but sometimes by smelling!). Skymark (Kobe) has some cheap fares, but the new carrier Peach (KIX) is even lower. There's always ANA and JAL, which you can sometimes get deals on too (I think we used someone's "birthday fare" once?). Sometimes it is cheaper and faster to fly to a place than to take a shinkansen (king of trains), sometimes not. If comfort and flexibility are a priority, shink is the way to go. If you need to save money, check out flights but also remember the cost of getting to and from the airport in your figuring!
International flights are predictably a bit more painful, and depending on where you are going, will cost a pretty penny more. Going international from Japan is almost always a flight, though there are some boats. To Korea, boat is a good option, but that's the only one I know. For Southeast Asia, I've had good experiences with the bare-bones low-cost style of AirAsia, though you may have to fly through Malaysia or something to get where you want to go. It's super cheap, but just know that the fare you are browsing does not include your baggage, food, or any other perks: those you have to add on as you go. Once you do, it's still pretty dern cheap.
My final confession on this topic will be that I've spent way too much of my life checking out the different options for how much it costs to get where by what different forms of transportation.