I also use MA, and the Jaguar emulator just frustrated me enough to abandon it. At least until someone else can provide a solid explanation on it.
I have had the same issues, or in many cases just got the emulator to show a text only bios like screen.
I had the emulator working alone somewhat at one point, then it just stopped.
While I give credit to the people who take their time to develop emulators and appreciate it, the virtualJaguar one seems to be one of the worst I've tried. I am not familiar with the Project Tempest you speak of.
3D0 emulation seems more solid (but was also somewhat of a pain to get working).
Sorry I don't have a solution for you, but I would also like to know a more foolproof way of setting up jaguar emulation in MA.