I heard somewhere that your factory warranty cannot be void if you perform bolt-on modifications. Basically, it’s up to the factory/dealer to prove the upgrade caused the failure. Best to get a lawyer who is familiar with warranty claims involved to help pull the paperwork together.
Being that you have a list, I can see how they would bring it up as a possible risk, but unless the drive line angles and load are significantly changed from what the factory ships, I'd say you have a strong case for getting it covered under warranty.
In the mean time, get a case open with the factory customer service folks. With all the ball joint problems the KJ has had, I've got two claims submitted for tire reimbursement. Would probably get a check if I had followed through with sending them my receipts...