I don't know anything for certain; it's really hard to find stuff related to what Jason used back then, but I think he probably used his Warmoth PJ bass (the one he's holding on the cover, maybe with EMGs by then) and/or BC Rich Eagle with a GK head and Ampeg 8x10...it's possible that he might have used one of Cliff's Arias as he's got it for the photoshoot, but his technique and attack is so different than Cliff's that it's really hard to tell sonically. He talks about his stuff a little bit in this video, around 4:45.
Since they recorded the EP a few months after the end of the tour for Master of Puppets, it makes sense to me that they would've used something close to his live rig in the studio. It's also totally possible that he used some of Cliff's Mesa gear to track with as well. I remember seeing scans of Flemming Rasmussen's notes from the studio during the tracking of AJFA that mentioned Jason using the GK head on that album even, but I think I read in an old Guitar Player article or something that he used a Steinberger bass to track all that stuff. Wish there was more info out there on this, Jason's tone is truly killer on this EP.