Emjay, what is it you hope to gain by supplying so much of your own wood? I can see the benefit of picking out your own top woods. Occasionally there's a really special tree involved, like the one you may have tumbled out of when you were seven, but that doesn't seem to be the case here. Beyond that, I don't get it. Unless you're looking for a wood that they just don't have, I would absolutely look to them to provide everything except the top, back, and peghead faces.
Personally, I really think Alembic likes to use their own wood. A special top is one thing, but unless the wood is from the tree you fell out of when you were seven, I think you may have a hard time convincing them to use any more of your wood than that. For example, what happens if a customer-provided piece of core wood is still a little bit green? Who is going to foot the bill for the hassles that come up if the thing twists into a pretzel? The neck would have the biggest risk of that, so I can see why they would absolutely refuse any customer-provided neck woods.
On balance issues, I think choosing ridiculously heavy body woods could help. You might end up with a 20 pound instrument, but it would balance nicely. Seriously, though, I would stick to the Rogue. If you are into it and have the dough, Valentino's custom with all the points on the body also has one of the longer upper horns available. I think you're looking at something like $1500-2000 to get that body style, though.
