Body wood, body shape, fingerboard wood, neck joint, pickups...there's a ton of different variables that will make one guitar different from another through a quality amp like Mark V. It's really hard to say which suits you the best.
I'm not saying that this is a bad question - I know from personal experience that, in order to truly enjoy your Mark V, you will also need a quality guitar. A cheap piece of plywood trash will sound like junk through it. But yours is a rather specific question, and I must honestly say I've no firsthand experience in those particular guitar models. Possibly no-one here has - and even if they did, their sonic preferences might not match yours.
Yes, in general ebony fretboard tends to sound a little bit brighter and produces tighter attack than rosewood. That's a relatively subtle difference, though.
Set neck and neck-through construction; either ought to give you very good sustain. Theoretically, neck-through is even better in that respect but not everyone feels that way.
What about the bridge? Are these both fixed bridge models?
Also notice that while both guitars have 'mahogany' bodies that does not necessarily mean that it is the same wood species. The term 'mahogany' is actually used for a number of different species - I know that the 'mahogany' in my Gibsons is quite different from the 'mahogany' I see in the average Epiphone (when they are advertised as having 'mahogany' bodies).
Also, no two guitars will ever sound 100% the same, not even if they are the same model, made of the same wood, same components etc.
(Yeah, I guess I'm not helping much...)
I would say go with your heart. In my experience, when making music, that is almost always better. When I buy something because its specs were, on paper, exactly what I was looking for, I always end up with some technically very good gear that doesn't inspire me at all.
I prefer to use something that inspires me play more and better, never mind if it's technically limited or frequently dissed on the 'net.
,
