i saw them at Slim's in SF last night and he was using a sunburst jazzie with tort pickguard and black pickup covers. for the encore he used a vintage white with gold ano pickguard. both had tune-o-matics.
this has already been covered, and i may as well mention he didn't use it last night, but i'm sure his signature jazzy is just a standard one with big frets and a tune-o-matic, like he said... better suited to his lead style than a stock jazzy set-up. apart from that it follows his signature purple/gold colour scheme as per his old purple marshall superlead stack. wasn't there a dino jr box set that was purple and gold too?
i basically think when all their gear got stolen he just splurged on himself at the fender custom shop and had a jazzmaster built to his exact specifications so he could keep rocking immediately, but then re-stocked his vintage collection while on tour. fender probably gave them an endorsement when he had the jazzmaster made, i noticed lou barlow had a '51 style p-bass and new fender bass amp instead of that daisy rock thing.
also, mascis may have many jazzmasters, but he appears to only own one set of clothes. same t-shirt as in that onstage pic, and he walked into the club wearing his adidas gear from the new video.