In the case of Gobin, I think that, while Gobin considers itself an independent state, the rest of the city would not. If forced to let MI conduct an investigation or levy a new tax, they would be resistant in that they would work as slowly and as listlessly as possible, doing only the very least necessary to accommodate the outsiders. This also means that the government of Ishka would probably want to interfere with the stubborn people of Gobin as little as possible, only sending in MI and government officials when absolutely necessary. I imagine that any Ishkan bureaucrat sent in to establish something in Gobin would be afforded the smallest office and least man-power possible by the shogunate.

As for On the Ropes, I'm liking the plot hooks, but it may be a good idea to throw in some more, just to really screw with investigator PCs. Maybe he had a big (some say violent) falling out with his wife a month or two ago. Maybe his best friend of years had been getting into some shady dealings with the Alliance and, if you look into it, he disappeared around the same time as his son. Maybe he owed a great deal of money to some less-than-legit drow loan-sharks.

Maybe he disappeared for a reason that nobody heard about. Maybe the pressure just got to him eventually. Maybe he's setting up a deal with the Shades to make sure the tour ends in a tie - helping to further diplomatic relations. Just bombard them with so much information that half the game is spent ruling out dead ends and filtering the muck from the gold. After that the exciting resolution, action, and hunting down of the culprits takes place, followed by a big plot twist at the climax.

I see Sphen as little more than a feature of the port district. It would be a nature reserve with druids and shugenja as rangers protecting the native fauna. Given that a large portion of its population is druid, and its culture seems built around druidic principles, to suggest that it would ever be any kind of economic power seems like folly. I imagine that the druids of Sphen would have a lot of support from the Wild; many may even be members. I expect that Sphen would be the Galapagos of Ishka. It needs some ecoterrorists bombing people trying to develop the island as condos to add enough spice for PCs to bother going.

As for an artifact in its bay being responsible for peace in Ishka, why, that's just silly. There isn't peace in Ishka. It has a long and bloody past of district-on-district conflict. It's only lately that politics has neutered their ability for any sort of large-scale internal strife. Many districts hate each other, and many citizens of Ishka can remember failed revolts and attacks.

The way I understand it, Ishka is built along one long river and the canyon it made, from the massive mountain lake (almost a freshwater sea) that is its source, to the great lake that lies at the end of the river. From there, the great lake at the end of the stream connects to the ocean by means of a few wide rivers, canals, and tributaries. It's something like how the American great lakes connect to the Atlantic. Aside from that, there are also gates to various ports and pieces of water around the world, as well as locales on the Elemental Plane of Water.

Also, for whom it may concern, since the generic undead templates are just templates and are all LA +0, they're all suited to both 3.5 and Pathfinder. When I make the generic elemental races later, I'll make 3.5, Pathfinder, and 4e versions of them.