This does all make sense...3 inches of travel with 2 inches compression and 1 inch rebound. My question is the limit of travel you have with 3,5 inches clearance and a 2 inch bump stop, with 0 travel being your center point, you have exactly 1.5 inches of travel either way and that's exactly when your suspension hits your stop...I hope I'm not missing something but it would appear as though your suspension is not being allowed to do it's full job. To me, and I could be wrong. it looks like a clearance issue. Upward travel is also dependent on load so when you've got a full tank of gas and passengers I would think the problem would be more noticeable, am I correct in that assumption?
I've thought about this so long and hard, I wish I was there to actually see it. Seeing it has got to be worth a 1,000 posts. Oh well hopefully they will get back to you tomorrow and have an answer.
Yet again, PLEASE, keep us informed.