It's been crazy at work, so I've only just got around to playing with the Miracle Man. The first thing I did, as suggested, was play around with the pickup height. This seems to have sorted the problem out perfectly. It might be that there's an intermittent fault with my soldering, so if the output drops again then I'll re-solder it, but as it stands I'm getting a great tone from the guitar. Comparing it to a Les Paul with Dirty Fingers, the V with the MM has the same round, full tone, but is just so much more articulate.
Thanks again for the advice everyone. Much appreciated.
Paul.