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I am currently undergoing a background investigation for a govt job that could take three more months, or a year and three more months... it tends to be a blackbox given the OPM backlog right now. I have also just been contacted by a Federal judge looking to bring someone on board very soon for about 11 months.

Issue - I am currently undergoing a background investigation. I received the opportunity to interview with a federal judge I would like to work for. Should I go on the interview with the judge and let him know that I am currently undergoing the investigation for the government job, but would like to work for him in the meantime? It would involve me leaving my current position now to move across the country to clerk for this judge for god knows how long (or short), and then to another part of the country for the government job - assuming he is okay with me coming on board.

I think you're suggesting you'll leave the clerkship whenever your clearance comes through, before your term is up? I guess it couldn't hurt to ask but I have a hard time seeing why a judge would want to take on that uncertainty.

I would contact the judge, let them know the situation, and ask if they still want to interview you. Letting them know ahead of time seems the most courteous way to approach this. (They may say no, but if so, they wouldn't hire you after the interview either.)

Also/or, is there any flexibility in your government start date? Can you arrange with them not to start for 11 months regardless of when your clearance comes through?