I toured in Albania fairly recently and thinking of going again in the next couple of weeks. It's lovely and as above the people are very friendly, English generally spoken, amazing landscape. Away from the tourist spots you can be fairly sure of finding places to stay and eat: the culture is based around going out and grabbing a snack or drink on the "promenade" which happens every evening in even the smaller towns. This is in stark contrast with, eg., Greece where away from the tourist locations it's like a ghost town.
Absolutely *do not* consider taking a train, unless you are up for an adventure of the type 2 kind. Public transport of the four wheeled kind is far easier and much faster.
I've also been close to the route you're thinking of in B&H. The walking route will take you over the mountains and some legs may be fairly long (I'm guessing here, but I know there are decent paths and mountain biking is popular). As for mines, yes there are lots left, and booby-trapped buildings. But if you are sensible they shouldn't be a cause for concern, any marked path is safe. Standard advice when in a mined area, don't step off the path (eg, to have a wee) and don't under any circumstance explore the numerous abandoned villages. Camp only on a known good location.
Borders are rarely a problem on foot or bike, you are expected to go straight past the queue of vehicles and with a British passport you will get through quickly. Make sure you get a stamp, but FCO advice about registering at a police station is 100% wrong.