Sure that's doable. Stereo TRS 1/4" jack on one end of at least a 3-conductor wire (neck p/u, bridge p/u, + Ground). Then on the 5-pin side, pin-1 Ground, pin-2 neck p/u, pin-3 bridge pickup. Nothing to the power pins-4&5. That should connect to your rig in the same way as your Series bass.
-- OR -- The IN-2 has "outputs" on the front and back, right? Those are tied together which means if your rack rig is using the rear outputs, you could use that Y-cable you already have and plug into the front panel "outputs". That would pass signal straight through to the rear panel "outputs", if you see what I mean. The only thing is, you'd still need to disconnect the Series bass from the 5-pin because in "standby" mode I believe that would short the inputs and stop audio from passing through the IN-2.
Jimmy J