The INF's are okay, you'll have to see what you think after spending some time with them. I just took Evo's out of a guitar with INF's and put the INF's back in, because the guy wants to sell the guitar and keep the Evos. Guess what? I think the INF's sounded better. But that's me, and I'm not an Evo fan anyway.
In the bridge, the Custom will sound great in that guitar as well as your Roadstars. You could go for a Custom Custom in the Mahogany one to give you some different character. And it will add back some of the upper mids that are LOST in the neck through construction. Remember there's a big Maple log running down the core of that guitar. So it's going to sound very different than a Mahogany bolt-on RG. It's not an "all Mahogany body" you're dealing with. If it were bolt-on, I would have said stick with the Custom, because you don't want to add that smooth midrange from the CC. Mahogany has a lot of that midrange naturally. But with your neck through, I think the CC would be better. But both are going to be great.
A lot of guys like the JB in Mahogany, but remember the
Maple neck through. The JB is too screechy in a Maple neck through IMO. Especially if you like the Custom in your Roadstars.
From Dimarzio, pickups like the Fred, Norton, and TZ are all good choices, progressively smoother. When people say the TZ is too thick sounding for Mahogany, it shouldn't apply in your case with the neck through.
In the neck, all your standards are usable. Although I'd recommend the Dimarzio Super 2. It's going to cut down the "nasal" sound of the
neck position on that guitar. A PAF Pro or Breed could be too smooth. (if that makes any sense) The PRS Vintage Bass pickup would be superb there, and visually match the Duncans. Also the Duncan Jazz, or Full Shred neck would be great.