Yes, you can still file jointly if you make an election to claim him as a resident. You would just need to add a statement to your Form 1040. See here Nonresident to resident
To enter information from Form 1042-S, it depends on the code in box 1 which you would enter into the program accordingly. For example, if it's wages or related, you would enter under Wages. If it is an interest income, you would enter as if you receive a 1099 INT etc. To see the list of the code, click here 1042scode and go to page 3.
If you claim him as a resident, he does not need to file a Form 8843.
Hope this helps.
[Edited 2/2/2019 10:06AM]
