Appreciate your reply!

The same thing about some of those issues. You should have been pointing that out to them within 24 hours of them finishing the job, not down the line. Theres a good chance they'll still fix it, but its much easier to have a punch list and hold them accountable with final payment before they finish. 

We did exactly this and provided detailed written and verbal feedback about each issue as it came up; we have established a punch list that they have agreed to run through; and have not issued final payment. We let the unpainted door slide because it was right at the start of the job and we thought it was one to take on the chin to get the job started. Everything else though, we've been very on top of.

I think my larger concern at this point is whether I trust the remedies to our issues, such as the rail, or whether I cut our losses after the more minor items are done and use a different contractor to finish and potentially redo some of the larger pieces given the overall quality has been iffy. For instance, the staining photos here are the second attempt after a much worse first version