It seems to often make it hard to get back where you were, like you go west and then east and end up in a different place. I don't know enough about z-machines to tell why.

Nothing to do with the VM. The game was designed that way, navigation is part of the puzzle.

Perhaps you could try making a map.

Not ZMachine related, not even with Inform6, where n_to, s_to and w_to e_to are pretty much self-explanatory. It's just that Dungeon/Zork/Zork-I-II-III were made that way.