So anyway I was promising everyone that I'd keep you updated on the various threads I opened with questions. I should begin though by thanking you for all your help throughout. You've been a valuable resource.
The threads were:
Current status: complete but for minor details.
In the end, my contractor did not fix the squeak around the girder that we had asked him to fix. It had been a mistake originally admitted to (but at the same time which he had shrugged off). The contractor had tried to fix it with, erm, spray foam.
A different squeak has appeared around the girder after we installed the closet, armoire and closet doors. The mistake made around the girder probably spans its length (i.e. they forgot to put some wood on top of the girder to give continuity to incoming joists), so putting weight around the area of the girder, as is the case with closet/armoire/closet doors can exacerbate the problem by adding squeaks. We'll have to live with it.
The contractor also did not have the floor people sand the floor. When we uncovered the floors, there were mill marks on virtually all the wood. Needless to say, we redid the floor with a third party and are very happy with it now. He must have done this to save time, because we had made him let the wood acclimatize longer than he wanted. I don't remember the acclimatization duration, but it was the one recommended by the hardwood floor vendor.
For the bath tub and bathroom tiles, our contractor used grout and not the other material which seals better. As a result, there were cracks in the bath tub grout through which I could sometimes feel a draft. This should tell you about how well he sealed behind the bath tub, yet another thing which we had asked for and which he apparently didn't do. We had someone else put the other material (forget the name).
Because of these mistakes, we finished parts of the job with third parties. This includes dishwasher/stove (my plumber managed to put a dent in my floors with the stove even though it has wheels), kitchen tile (job was good), fireplace.
(DK Fabrications in Long Island did a terrible job with the fireplace. They put only silicone below the hearth -> squeaks. They took it out. They were going to reinstall, but declined to use the thinset chosen by us. We installed with someone else while DK was to remain responsible for remeasuring and returning the parts. They made mistakes with the measurements resulting in various delays and made no effort to be expeditious about the multiple deliveries, being late by hours at a time. I don't recommend them. They were giving me the usual "this is the first time this ever happened to us", which reminds me of my land lady, who had said the exact same thing to us when we asked for more heat in winter, and then to our surprise we found out she had said the exact same thing to a neighbor with the exact same complaint. That should tell you all. I warmly don't recommend them.)
A final payment for the contractor was retained and while we're not sure if we're even or if the contractor still owes us money, we're going to leave it at that.
Our thoughts on this contractor? He disregarded some of our requests, he hurried to finish his job at the cost of keeping us informed and giving us the opportunity to choose, he wasn't on site all the time like he had promised. (He wasn't on site when the girder mistake was made. Per his remark, he was building his countryside home around the same time he was renovating our place, so I suppose that's where he was. Go figure.)
Lessons learned? Although our contract was quite thorough, we will be an order of magnitude more thorough with our next one, if we get to that. We'll have to tell the contractor where to use grout, the electrician not to put a 10 A towel rack on a 15 A circuit shared with the central outlet in a small condo, where it's most likely we will want to use our 5 A vacuum cleaner, and so forth. Probably an architect will have to put everything on a plan. And maybe we should have someone on site all the time, chiefly a project manager.
Let me know if any questions come up.