...having the logo on there and trying to explain to folks that its actually not an Alembic was discouraging
Yeah, that's kind of a sticking point. Even though this IMO doesn't qualify as a full-blown forgery or fraud, this is sounding less attractive, just because of what it's not, even though the Series electronics and parts have considerable value alone.
Here's where I'd draw the line - (purely hypothetical) if someone owned an Alembic bass, that had something tragic happen which rendered it unplayable and unfixable in the whole, then I wouldn't object to someone having a reproduction body made, and putting the original parts into it. Were it mine - I would make every possible effort to graft the original body wings and/or headstock onto a new neck rather than simply do a switcheroo with the logo. One thing the guy I apprenticed under stressed to me almost daily - wood is forgiving. The neck-through design adds another layer (no pun intended) of difficulty in an already complicated repair, but it can be done. Even so, I would not under any circumstances try to pass it off as anything other than precisely what it was. (not that that's the case here)
But really, if you're going to that much trouble, (and no doubt expense) why not just send what's left of it out to the Mothership for a proper fix? Just my limited experience with the Staff there is that they are more than eager to help keep instruments that bear their name 100% Alembic-spec. If I went home today and found my Persuader in 3 pieces, it'd be in a box on the next Brown Truck bound for Santa Rosa, even though I'm completely capable of fixing it myself. Obviously, somebody else went a different route with this one.