[SSDan]

Much of the times these ticks and clicks we hear are probably normal operation or maybe a header leak. I don't think that is the case for you unfortunately. To my ear that indeed has a very mechanical valve train sound much like a lifter/push rod. However as mentioned its worth eliminating the possibility of a header exhaust leak. I've seen a lot of people fix their engine ticks with a new set of exhaust gaskets.

The headers, tune and e85 sensor certainly can cause a dealership to deny warranty work. But who knows - some dealerships are willing to turn a blind eye to mods that are not likely to be directly related to the issue. I'd say take it in - no harm in asking - until you do the answer is by default "no".

Good luck and keep us posted.