I don't believe there is a "best" way to balance enemies. This is a pretty generic response but it depends on too many variables. I wish there was a magic formula to do the job but nope :(
All I can say about scaling is, if you let all your mobs dynamically scale up to your party's progression, you kill off the sense of character progression in my opinion. PCs should be able to kick ass if they ever return to the areas they left far behind. Of course, it is a different story if the mobs change for a good reason, e.g. tougher reinforcements, evolution, transformation etc. In that case, you can just add better rewards but you should still explain the change to the player behore they enter the area. Otherwise, it would be an annoying surprise rather than interesting.
If a simple slime from the beginning of the game puts me down when I backtrack for a chest or something though, it would totally hurt my interest in the game.
You said there was no sense of scale or level in the game. You don't need to have a level based progression in an rpg but there must be a sense of progression, like new skills to obtain as the characters move on. That may also apply to monsters too. If you imagine the game world to be dynamically evolving as a whole, monster may learn new skills as well as long as it makes sense in the game's own reality.
As for eventing, you can set checkpoints at certain progression spots (for example, end of a major main quest) by turning on switches. In the enemy events, start new pages and condition them to those switches and change the troop on each page. Yes, you will have to create multiple copies of the same enemies but if you want them to be challenging throughout the whole game, you will need to create strongers skills and statistics for them anyway so you are actually creating new enemies with common skills. It is just a matter of adding them to the database after that.
