First of all, one can become licensed with a masters in clinical psych. You just need to make sure you have all the appropriately coursework to be eligible for the licensing exam.
Yes, it can be done from a MFT, but this is not optimal, especially in your case. The course work is notoriously easy in a MFT program, and will not carry the weight as a masters in clinical. It's a very clinically oriented degree with few if any research requirements. And you need this badly in your case. Keep in mind these are 2 different fields, utilizing different skill sets with different orientations towards understanding psychopathology.
I am not sure why you really need the Ph.D for your goals here. You want to do counseling primarily (which you can do with the MFT or MA in clincial) and maybe resesrch on the side. If you are in a hospital setting or group practice you can pretty easily join and assist in research with your doctoral level colleagues. You probably wouldn't be the one in charge, but you could certianly be involved.