Hi fjs1962,
Thanks for coming back to this thread during the years so I can find this post. I used to have a shuriken and just got a jtv-59. Both have the same problem with the low E string. It's definitely thinner and brighter compare to other strings. I thought it was the pickup but since the new guitar has the same problem, I 'd say it's a design flaw. I will try to play with the workbench and see if I can make it any better.
I have a theory. Maybe the groove on the low e pickup is too small for the string so the string doesn't have a good contact with the pickup. A thinner gauge may help? I may try that later.
