I would agree with the others...call him, I just talked to him last week. I'm sure he would be happy to hear how his instruments are "getting around" in the world.
All of the below referenced info is here: http://www.birdsongguitars.com/info.htm
or here: http://www.birdsongguitars.com/owner.htm
I've seen cloverleaf tuners on C-basses before, it's possible they're original, but I don't think I've ever seen them on a Cortobass.
The battery box is definitely aftermarket, I'm betting you someone jacked around with the electronics trying to add a preamp or something.
The EMG select pickup WAS at one time standard on the Corto. This is from Scott's website...
"A few pickups have been used: The neck pickup on most basses has been a Lace "gold sensor"; the CortoFusions have a specially chosen humbucker used, mounted and wired so completely differently than it was designed for that brand & model names are irrelevant. Contact us for details. The current Hy5s have Kent Armstrong soapbars and we love them. As for bridge pickups:
The EMG Select SEHB humbucker, a humble but fantastic sounding pickup by a company that wouldn't give us the time of day... (pre-2006)
The custom-designed Birdsong "Punchbucker", a further refinement of that tone. The company that made them for us decided our orders were too small to bother with and stopped the supply. And you thought this was easy? This is why most companies just build P-basses and be done with it. Sigh. (2006)
The high-output Lace we put in some single pickup basses needing a growly aggressive thing since it doesn't play well with others...
and a milder Lace with a great tone we've used as standard equipment since early 2007."
Also from Scott's website regarding the zero fret:
"The zero fret is a fret directly in front of the nut, you won't even know it's there when playing. To my ears it makes the open notes consistent with the fretted notes. It also supports the downpressure of the string, taking this task away from the nut. And it gives very low action at the nut. It's not found on many American instruments because (ahem) Leo Fender didn't put it on, but it goes back generations in European stringed instrument luthierie. I like it, it's a premium feature I can put in there for you so on it goes. Some inventory builds & one-offs don't have one, but most Birdsong basses have it."