Nice score!

Yeah the 9' beds like that weren't really designed to go on trucks with duals, so winging-it is a good option when you tub the bedsides and widen the fenders lol. As for the tire to bed clearance, I'd say whatever you think looks good/right.
Funny enough, I picked up a '60s Chevy 9' bed. Also green. Also turned into a trailer haha