I'm not sure that dual 2.5's wouldn't actually flow more air than a single 3" would, in theory. But a single 3 should still be plenty for what you're talking about. Unless he's going to mud-bog or sand race it. As long as it's hooked to a high-flow muffler as well, he should be happy with the performanc, and the sound.
I think that all the mufflers recommended above are good choices, but if your Dad is a die-hard Flowmaster fan, then stick with that and keep him happy. And yes, a two into one Flow can still sound damn fine.
I'm more a fan of the straight-through designs like the Spintech and the Ultra Flow and the Magnaflows myself, but there's no denying that good old classic V8 sound coming from the correctly matched Flowmaster.
Don't go too small or too few chambers and you should be golden. Stay away from the 2-chamber versions if he's even remotely past his teenage leangings. Go with a 40 or 50 (or even a 70?) series and if you intend to take it on long trips with the hard top on, go with the Delta-Flow version of whichever model you choose.
Oh, and good luck. Like you said, don't over think it or you'll get grey hair before he does. But then again... Overthinking is the fun part of building up a Bronco. Then, after all that, you get to second-guess your decisions for years to come. Until you try something different only to decide that you really liked the way it was before.
It's a Bronco thing...
Paul