Since she is not paying tuition, there is no need for a 1098-T. Also, to claim an education credit, the school has to be an eligible education institution.
Yes, they can file jointly for federal and yes her stipend and housing is taxable. Tuition is not taxable.
Yes, if your son earned money in NJ and CO and a resident of CA, the would file a Non Resident Return for NJ and CO and then file the CA return claiming a credit for taxes paid to NJ and CO on his CA return.
Yes, if she is only temporarily away from VA, she will need to file a VA return as her resident state. Your resident state will tax all income from all sources worldwide. If you are being taxed on that income by another state you can often claim a credit for it, however since she is not being taxed by another US state, she cannot claim a credit for the taxes paid on her state return, but if she is paying taxes to the foreign government, she may be able to claim the credit on the US return.
No, they do not have to file jointly for the state returns since they were not residents of the other states.
You can use TurboTax Deluxe or higher.
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