Correct, it had absolutely nothing to do with the new tray, installing the tray only led to the discovery. In fact, I think the new tray actually provides additional underside clearance as it is perfectly flat on the bottom. For clarification, this is the support for the main battery, the secondary battery hangs just behind the EVO bracket in a little cubby bolted to the bottom of the stock battery tray. Also, I don't believe movement of the body/isolators has anything to do with it either as the EVO bracket would effectively protect the shock head from those types of movements. I believe it is actually the rotation of the shock head that causes the interference.
Here's what appears to be happening... Sitting static at ride height, the top of the EVO bracket just barely touches the bottom of the battery tray support (which is part of the body). When the coilover is straight up and down, there is little to no contact as the radius of the shock head is the same height as the bracket. The shock head however is not a perfect circle, in fact I'd describe it as trapezoidal with a rounded off top. So, as the shock compresses and the head rotates forward due to the travel path of the control arm, the effective radius of the shock head gets larger. This causes the shock head to protrude above the bracket, thus scraping on the bottom of the battery tray support. I'll mention too that this is pretty much from daily driving, my Jeep has sadly only been off road once so far, and it was a tame trail at that. No extreme articulation or anything.
I'm not looking to play the blame game here. I'm not pissed off. That is not the point of this post, please don't be so defensive. I think this issue was caused by EVO trying to squeeze every last bit of travel out of this set-up, and I commend them for doing so. After all, that is what we're all after. As I mentioned, I have an early kit. There were a few other clearance issues I talked to Andrew about during my install that he said would be addressed in the CAD design. I'm just curious to see if anyone else has had this problem, if it has possibly been addressed with a minor design adjustment, or if I just have an odd-ball JL...