My opinion: 0.040" will work fine with your motor from a clearance stand point. I would definitely prefer that over 0.060". It may, or may not have detonation problem, but I believe that I could work through that based on the fact that you seem close now. Knowing the cam ICL could have a bearing on the detonation outcome along with several other items. All that said, now that its all together, I don't know if I would go chasing after this.

What seems odd to me is that you wanted a motor with 0.040" quench but you got one with 0.060". How did that happen? FWIW, whether its the motor build, or the distributor, the more ownership you take in it, the better the results will be.