Many months and gigs later, I still wasn't happy with it. Sometimes it would sound ok, but mostly not, and with the pickups screwed right down the output was weak.
So I had a harder look inside and realised the Kent Armstrong rebuild pickup at the bridge only had one coil wired in and was wired with the polarity backwards. Having swapped the orginal wires round and wiring the other coil to the back of a pot, it sounds right now, I can raise the pickups and take out the bit of foam.
As there is an out of phase option on the pickup selector anyway, I can't really get my head round the electrical effect of the previous wiring.