I've ruled out trains really as a form of travel (although.... maybe) because the time when the story takes place is a momentarily bad one for the human race. Pokemon are being driven mad by something and it's driven the humans back into their cities to defend themselves (the plot of the fic is the main characters discovering what is driving the Pokemon mad, and fixing it), which is why they're not just going to drive from town to town. The designated trainer routes is a great idea, since travel in this timeframe would be heavily regulated and guarded for people's safety, I'm going to use that, thank you!
With the distance between the town, I google mapped the largest distance (which I believe was between manchester and brighton, although I'll have to refer back to the makeshift map I've made up), and it turns out according to Google it's a 76 hour walk (or so). That's about a week travel time, and I can change up the order of the gyms to cut out back travelling. Looking at these considerations, I might research a few more towns and see if I can turn the Journey into more of a spiralling inward towards London perhaps... The distance isn't so much of a bother (the UK, England in particular, is actually really small, TIL), as the backtracking that they'd be doing.
Does this make sense or am I rambling? Thank you for your great feedback though, it's given me some wonderful ideas
I draw pictures of Pokemon on Paint.net and write lame fanfictions. That is all I have to offer.