2007 & 2008 Lifetime Limited Powertrain Warranty

I bought my 2007 used from a Ford dealer last April with a 1 month/1,000 mile warranty. I thought the warranty was acceptable since it was a 4 year old vehicle with over 60K miles on it. They did replace a harness because the airbag light came on and stayed on.
Water pump started leaking, but I didn't realize it was the water pump right away, I thought it was condensation from running the AC. I got my hopes up when people started talking about the lifetime warranty from Jeep, then found out it was first owner only.
I was going to replace the water pump myself, but then it stopped leaking on its own. I'll probably still replace it, though. It's not too expensive and there are several threads about people having theirs go out around 30K, so mine may already be on it's 2nd and in need of a third...
)
Anyone had any issues with going in for the inspection with axle modifications? I went in to mine today and they told me because my axles have been modified, it voids everything else as well, include engine , transmission, and tranny. I don't believe this is correct, but can anyone verify either way? I'm supposed to go back in for a reinspection in a few weeks because I didn't have my front driveshaft in as I'm currently replacing it.



