Hi Steve, congrats on your new MK 5-er! I'm the still very happy owner of a '99 Jimmy Johnson Signature 5-er equipped with AXY5/6 pups & Anniversary electronics. As a big fan of JJ's playing I've been looking for a similar sound from well before (finally) becoming an Alembic owner and the biggest leap forward in the right direction I found was switching to GHS Boomers on my then Dutch built 6-string (which did have Alembic pups & gut, but from a wood perspective was way off).
As for settings: my Anniversary controls are 2x vol rather than vol + pan so you may have to tweak a little differently, but (on my headphones) I get pretty close to JJ's sound as follows: neck pu full volume, Q-switch off & filter almost fully closed; bridge pu: volume rolled back to abt 75%, Q-switch engaged and filter fully open (gain pots inside cavity both fully open). When I want to make the sound a bit bigger I open the neck filter to halfway (and then regret there's no master vol to keep me level, but hey, that's a different [price] league altogether). In the thread Adriaan linked you to I believe JJ somewhere states he uses everything full up with the bridge pu getting some emphasis from the gain pots (which I believe are accessable thru the control plate on a SII, sigh) I now btw use DR Sunbeams (Tight wound variety) which are a tad milder than the Boomers, which imho makes up for the humcancelling pups sounding a bit harsher than single coils (which are standard on JJ's Series II basses, sigh). As a small consolation: I once had the pleasure of talking to JJ at a Michael Landau gig and he told me that his 3 SII's were ordered to largely the same specs but still all have a character of their own. The nice thing about Alembic I found is that there is so much nuance in even the smallest of settings changes, no doubt you'll find a whole palette of sounds you'll grow to love. Take care and happy New Year (shouldn't be an issue with a new Alembic?), Reinier