Your mistake was beginning before you had a firm plan. This not only will increase costs for you as any contractor can only give you estimates on firm items, but it also sent the message to your contractor that you cannot be relied on to make decisions and it's best to wait you out while you change your mind several times.

If you don't have the money to pay for your changed mind, then you go back to the original plan--if the original plan was realistic in the first place. But, you should also have had at least a 20% contingency fund to pay for unexpected expenses and that should take care of some of the changes unless you started moved plumbing around or went from $5 a square foot tile to $50 a square foot tile. And you should have relied on national average numbers for your ballpark estimates, even if you were getting lower specific numbers because of locale. The national average mid-range bath remodel, replacing like with like, costs around 16K. An upscale one, 53K. A midrange bathroom addition, such as a master bath, costs around 40K. An upscale one, 76K. With you moving things around, your costs should be closer to the second than the first.

PS., The contractor may also have wasted a permit trip if you have changed things. The AHJ usually wants a complete set of construction drawings before issuing permits. Any changes at this stage may involve getting additional permits, or voiding the original permit entirely and applying for a new one. It depends on the locality. But, your contractor also may have jumped the gun on the demo if he did that first without receiving a permit! Not a nail should have been touched without the bureaucratic signoff!

I appreciate you insight. After reviewing the slight changes and speaking with the architect, the change only results in a few hundred dollars because two walls are being moved slightly. It's totally gutted so moving won't be major.
What concerns me is the contractor is blowing us off (before we even contacted him about the changes) and is trying to squeeze in another job. When the workers said they would not be at the house last Friday, everyone thought they'd be there on Monday. I emailed the GC to ask what he needed for Monday. That was when I was told no workers because of permits. And no show today either. The GC received the slightly changed plan this morning after the crew would have left.

Well, Friday was a religious holiday for many people, so it isn't surprising that they didn't work. It also may have been impossible for them to pull permits.

As others have said, you shouldn't have started without final plans and permits.

Bill,
I would have agreed about the religious holiday and had no problem. However, the last thing the plumber told us Thursday before he drove off is they would not be there Friday because they were installing a boiler and they planned to come back Monday.
It wasn't until after the second floor was gutted we saw the possibility of making both bathrooms be able to fit a standard 60" shower rather than the current 54". The MB actually had a hacked-off 4-1/2' tub crammed into the corner. I don't anyone knew what was behind those old plaster walls until they came down.

That is fine, but changes = delays. That is just how it works. There is absolutely nothing wrong with adapting the plan as circumstances dictate. Just remember that you probably don't understand the full impact of "small" decisions on the overall process. eg you delay 1 thing and it causes a cascade of other delays. Say you push the framing back 2 days. Those guys might be scheduled for another job and can't get back until the following week. The the plumbers need to be rescheduled, then the electricians etc. At any step you can run into additional scheduling conflicts. If you are making changes, that is just one of the things that tend to come with the territory.

bill,
Yes, I absolutely agree. We had no intention of changing anything. when the architect came over the house Friday because there would be no workers, he took a look at the framing and said there would be problem changing the two baths to be able to put in the 60" showers. The GC had no clue we were even thinking about it until today. Where was he?
The contract calls for an end date. If they aren't working and they haven't begun to do anything after the gutting, I don't see how they can get it done.

Well, they probably won't. Just get used to it. When you change things on the fly, that is what happens. Heck, even when you don't change things, there is usually something odd that comes up and delays the timeline.

BTW - that "end date" on your contract is an estimate. You aren't going to be able to hold them to that at all. You need to just concentrate on making sure they are doing good work to your satisfaction and forget about the timeline. If it takes an extra couple weeks to get the finished product you want, so be it.

"BTW - that "end date" on your contract is an estimate. You aren't going to be able to hold them to that at all. "

Especially if you are making changes at this point.

For every project, there is the schedule you talk about with the contractor, and there's the schedule you plan your life around. For the latter, take the contractor's schedule and double or triple it. If he's done sooner than that, consider it good fortune.