From what I see so far, you should do the following:
1. File as married filing joint. It is quite unlikely that filing married separate would be better for you two. The fact that your spouse earned no money is not a reason to file separate unless you have an unusual situation.
2. It appears that the music therapy organization sent you two 1099-MISC forms: a wrong one and then a corrected on (for about $16k). The company may or may not have remembered to check the "Corrected" box at the top of the second form. If they did not check the box, this is likely the reason that the IRS taxed you on both 1099-MISCs, because the IRS had no way of knowing that the first 1099-MISC should have been superseded by the second one.
3. The nursing home sent you a 1099-MISC that was approximately correct.
4. Did the IRS letter ask you to send the 2017 tax return to a particular agent or office (as opposed to the general address for your region)? I would recommend replying to their letter with the explanation that (1) the first 1099-MISC from the music therapy company of $10,500 was incorrect, (2) the second 1099-MISC of $16,600 should have been marked as "Corrected" but was not, and (3) there was another 1099-MISC of $6,000 from the nursing home that the IRS may not have. Add your tax return itself if the letter asked for it.
5. Complete your 2017 return in TurboTax using the second 1099-MISC from the music therapy company (of $16,600) and the nursing home 1099-MISC of $6,000. Don't enter in TurboTax the first incorrect 1099-MISC of $10,500.
6. Also, with the letter, include copies of the two correct 1099-MISCs (the IRS evidently doesn't have a copy of the nursing home 1099-MISC), as well as a copy of the incorrect 1099-MISC (mark on it that it should have been superseded by the second 1099-MISC was that should have been marked as "Corrected" but wasn't).
I am mildly concerned that you say that the 1099-MISCs are not exactly the same as what you were paid; however, the two I have pointed out appear to be approximately correct, and you don't have time at the moment to haggle with either company to get really really correct ones.
It appears from your description that you will owe only self-employment tax anyway, so this is likely to satisfy the IRS, at least for the time being. Good luck with it.
