IMO the most important thing to do is cc them. Pistons are above deck but the cc for them can be figured out as well.
That and knowing the flow numbers will let you pick a cam.
There's various published flow numbers for X-heads (stan weiss has a big collection, there's also some here on FABO). So if you can't get them floewed you still can have an idea. As 66f posted a good valve job will go a long way.
Any matching between the intake and heads should focus on possible offset of the side walls. There seems to be alot of variationin port to manifold bolt holes from head to head. I don't see an issue if the intake side is a little smaller. Arguably some advantage in keeping velocity up and anti-reversion. I do see a problem when the air flow along a side wall or roof of the intake has to make a step to get into the head. Exhaust side can have the same alignment issues.
