I read that I need to get a conditional used permit if the STR is more than 90 days.

It is not "ready" to rent until those renovations are done and you haev a C/O or permit sign offs ect. 

The rest of San Diego still has STR permits available.I am hoping for a good peak season to offset how poor the off season was.You are doing something very well if your ADR is up (or you previously was doing something terribly wrong). 

This tenant has been great, and I want to encourage them to renew, but I’m also concerned about potential risks if I permit subleasing.Can anyone share their expertise on subleasing?

switch the zoning or rezone to hotel or a permitted grandfathered zoning instead of looking for the license go bigger and get it permanent not just one unit. loophole but very powerful how a lot of condo development is moving forward in miami they are hotels technically 

I have my STR in Kona, so I'm your competitor.I handle everything, when I bought the condo is not even have permit, so I purchase with LLC DSCR loan, then I apply for the permit, takes a while, everything is so slow in the island.

Does anyone have experience with permitting with the city?

I was able to negotiate a package that included the land, some of the materials, and the permits to build it.

In general, you will need to have a travel permit for each county the home will travel through.

Plans, permits also as they can take some time, I am unsure of how long in Hot Springs.