Harper and Ed are right. Good answers.
But Inspectors are kings. You were the jackass (no offense as I think all of us including me were the jackass to a "overzealous" inspector).
Here is the deal there are generally no rules unless you are in a city big enough that has multiple head inspectors. I doubt Clearwater fits that - I am sure there is one person in charge of residential permits there.
Here are two things that you didn't think of:
When you get a permit NEVER EVER EVER DO SOMETHING ELSE IN THE HOUSE THAT EVEN SEEMS LIKE IT COULD NEED A PERMIT IN THE LOOSEST SENSE - AND DEFINITELY DON"T MAKE IT VISIBLE. You did the worst thing you could do - open up walls you are not doing permit work on. Here is the deal the city could have a rule that if the inspector sees it, make you pull a permit. Or the inspector could just be a jerk and spinning you around in circles. If I pull a permit for a kitchen - I make my guys hide the new toilet and sink we bought for the bathroom. No damn way I am pulling a permit for switching out a toilet. But on the other hand if inspector saw this stuff I would totally be expecting him to make me pull permit. When you do work like this often, there are expectations.
You didn't use any "preferred" workers. Not saying this applies to you. But most cities I work in now have plumbers, electricians, hvac, whatever and it sure seems that things get OK'ed way quicker if you use one of the "preferred" guys. You don't use them, sure if you do good work it gets cleared. But it takes longer, there are more steps, inspectors often find "other things needing a permit", and simple things that you can remedy on the spot often take another visit. It's the game.
What can you do:
Have an honest conversation with the inspector. Just ask the guy what he wants done on your part, what permits he wants you to pull and so on. Just lay it on the table. If you don't have money for some things tell him. You cannot bargain with this guy if you don't understand the worst case scenario. If you can negotiate you need to know what "the worst" looks like. You have to understand there is no way out of this. You can delay things but if you just stop communication the city may fine you if you do not let them see your house - and you for sure will never be able to sell house. You let this go and just finish up... you will be opening up every wall in your house and pulling permits for stuff you never touched. Honestly the only way you can get lucky is this inspector gets a new job and you fix things up before new inspector takes a look - are you banking on that?
Also expect to have good answers to questions. You have walls open? Why? If you aren't changing the walls you need to have a good reason why they are open - drywall was damaged or torn down wallpaper that didn't come off well (examples). You might be required to pass a finish inspection where they make sure you use correct wall covering and it is secured correctly - drywall inspection.
JUST IN CASE YOU REALLY HAVE OTHER STUFF YOU WANT TO DO (not saying you should do this but if you do..) ONLY CHANGE THINGS IN THE WALLS RIGHT BEFORE PUTTING UP THE DRYWALL. Do not change framing, plumbing, electric, whatever or even look like you are thinking about it.
Hot tub time machine... Go back to that day at the permit office. Pull that permit to turn your box right. Done. That's all you needed. You already had a finished bathroom. If you are 100% secure in your ability to redo it correctly the inspector is not helping this equation. You should have did the original work, got it checked, and got the city out of your house.
Fines: There isn't an answer for this because it depends on city, inspector, scope and just whatever. Most likely you get some small code fines. This could be in conjunction with a "stop work order" or the "stop work order" could come first to push you to getting the permits. If you do work on your house while being issued a "stop work order" you might as well build a funnel to your bank account to the city. You will get a big old sticker or paper put on the front door/window announcing to the entire community that things aren't right. This is probably as severe as your situation could get. There is always a chance that the city could deny your CO and boot you from your house but that would really be pushing boundries for person already living there.
The most likely outcome is the inspectors just forget about you. As long as you don't keep calling them back, they won't show up. Your permit will expire and they will forget about you. Without you acting like a complete ass to them there isn't a reason to "fine"... but they can - I am sure there is some sort of code violation you are committing, aren't we all. If you do get fined you have to pay it. They will just start mounting fees on fees and they could put a lien on your house - this is severe and doesn't happen often.
Selling the house:
Scenario #1 - dumb city, dumb inspector (buyer), and house performs great for new home owner. You could possibly sell it and be off the hook. Very very low chance.
Scenario #2 - dumb city, smart inspector... He pulls recent permits. Sees that this one never passes final. Calls city on it. City sends inspector out to your house and city denies CO until permits are pulled for past work. City will make you open up every wall. The house you just got ready for market is now in shambles, you are out thousands.
Scenario #3 - dumb city, smart inspector... He pulls recent permits, client decides your house not worth gamble. Now your agent has to tell every potential buyer that the house still has an open permit and work that the city never signed off on or agent can/will lose license. Price of your house plummets.
Scenario #4 - smart city. A lot of cities plug into real estate databases with house spec sheets they maintain. So if you add a bathroom without telling city, city will see the extra bathroom on MLS, then they will have inspectors pay you a visit. Same thing flagging houses without final inspections. No idea if Clearwater does this but a lot of cities do. You will open wall and yada yada yada.
Scenario #5 - dumb city, dumb inspector, house has issues. Home owner sues you and your agents. They can probably attribute any issue other than roof and shingles to you possibly doing work. (not saying they would ever collect because that would require them to prove knowing negligence. but this could require retaining a lawyer and court appearances.)
What are your options:
Finish up and work with inspector. You can probably space this out pretty far - most permits give you a year. And if you are pulling for more stuff your clock starts over when you pull new things.
If you will be in the house a while, try to let permit slide. Hope inspector moves on. Very easy to play dumb with new inspector and 99% of the time new inspector could care less about old inspector's unfinished stuff - more crap work for him. The you just pull a very simple permit, something kind of pertaining to the stuff that was unfinished from previous.... boom you got a final as far as city is concerned (not saying I have done this but it works). You run the chance of that inspector never leaving and putting you in an odd position when trying to sell house.
Sell house to a "partner". Given that the work you do is good and no safety issues you can in good mind sell to a partner, who can then re-sell without fear of city coming in about permit. Almost zero chance a city makes a new home owner finish an old permit - it makes the city look terrible. It can happen if the city feels you two are in cahoots. I have never done this, I have seen it done many many times and have bought houses like this.
I don't know everything going on but I have to think option 1 is the easiest right?