You're correct about the Pit. Seems like the Alchemist and Magic Shops, as well as Town Hall and the Guilds, are in another section. Town Portal drops you outside the Tavern there, but to get to the Weapon and Armor Smiths, you have to jump over the fire chasm thing to get to the walkway over there. The Bank is toward the back, as is the Training Hall. Though, you can go around the Tavern and shortcut through the wall behind the Tavern, IIRC. I think the Temple is also near Town Hall.
As for Deyja, the only shops there are the Magic and a couple of guilds, as well as the Temple. Tavern and Stables kind of a hike away. Also, Town Portal doesn't drop you anywhere there --- unless you have Lloyd's Beacon, you have to Town Portal to the Pit, then go through the Hall Of the Pit and head outside.
I can't believe I remembered all that; it's been a LONG time since I've played MM7!