The Jem singles are quieter than the humbuckers, I've noticed that in all my Jems except the VWH. The only thing you can really do, is to raise the height of the single and/or lower the humbuckers to try to match them better. There is a chance that your single is going bad too though, there shouldn't be a massive difference, although, when I got my DY, the single was so low, it was flush with the pickguard, and that isn't right! Don't get tooooooooo close to the strings though, or you will lose some comfort, as well as the magnetic field of the pickup will cause a reduction in sustain as it will lessen the amount of time your string will vibrate.
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