I prefer to stick with more traditional tonewoods... I'm used to the tone and feel of rosewood. Ebony I don't have much experience with. This is basically an attempt to get a semi-hollow sound like a 335 or the HBII but with the ergonomics and playability of the Cu24. Maple top and back will probably make it plenty bright, so it's a question of how much more ebony would add to that, and would it be overpowering?
This is a great topic for discussion all by itself.
I had three nearly identical Singlecuts in succession, one with an IRW fretboard, one with ebony, and one with BRW. I'll get to these in a moment. Some additional background:
I've also had The Artist V with an its fretboard, and many similar CU22s with the rosewood boards. I've had maple fretboards as well. And of course, lots of other electrics & acoustics with either ebony or rosewood. But I think the best comparison is model by model, with the main difference being the fretboard, and the PRS model I've had with all three traditional fretboards is would be the Stripped 58/SC58/SC245, which is basically the same guitar in different trim and with different fretboards.
Of the traditional materials, the warmest tone will be the IRW. If it was food, it'd be chocolate. The BRW is a bit snappier and more articulate at the note's point of attack. In food terms, chocolate with a cinnamon swirl, because you taste the cinnamon on the tip of your tongue before the chocolate overpowers it. The snappiest of the three, with the fastest attack will be the ebony.
I honestly don't think any of these woods is "brighter" or "darker" even though that's folks' usual impression. What I think is happening as this: every note has an ADSR envelope - that is, attack, decay, sustain, and release. An ADSR envelope looks like thi
A note with a faster attack has a steeper attack portion, and if the attack has even a slightly higher amplitude, it's often going to sound brighter and more percussive. The slower the attack, the warmer it will sound. A bowed instrument like a cello will have a less steep attack than, say, a piano. Of course, the decay, sustain and release parts of the curve also affect this, but I believe that the main contribution of the fretboard is the instant of note attack. Just my thinking on this.
So picking a fretboard wood is, to me, one of those tone questions. I've come to prefer Rosewood on my PRS electric guitars because a slightly slower attack with perhaps less relative amplitude compared to the "D" and "S" periods of the envelope suits my less percussive, less strummy playing style on the electric guitar. On acoustic, I still prefer ebony.
My conclusion: If you like a very articulate, very well-defined note, go with ebony. If you like a nice fast attack and that articulation, but want a little warmer sound, go with BRW or Madagascar (which comes on a lot of PS models these days, and also sounds very cool - for some reason all 3 of my PS electrics came with it); for the warmest sound, go with IRW (though I realize that very few people pick IRW when they can get the other stuff on a PS).
My impression of cocobolo (this from playing acoustic guitars with it) is that it's like chocolate with a little caramel swirl. But I haven't had it on an electric.
Mainly it's just what I'm used to, but I assume the sealed construction offers better protection against the elements. I've never really understood what the advantage of open-gear tuners is supposed to be. I know people like them because they have less mass, but... why is that a good thing? What's the trade-off?
I think the open gear thing is mainly a cosmetic choice, but the main advantage to the Phase III tuning machine is that it's actually a better machine in its operation, IMHO. The tuning is more accurate with less slop, and it seems to stay in tune a little longer. It's really a very fine tuning machine.
Unless you're playing in a sandstorm, I can't really see a problem with the open gears. I have had them on a BUNCH of recent PRS guitars, and they've never gotten so much as a piece of lint on them.
These modern designs don't need to be lubricated with grease or petroleum jelly like the old machines in a bygone age, so they don't attract dirt.
I'm sorry about that, and mean NO disrespect to anyones guitars at all! Here goes. 
(Unless of course, you're going ALL natural, like my 97 Custom 22).
