The squeaks on the leaf springs might be crap that has built up between them. I had this happen on a previous truck. The clicking you are hearing is most likely the waste gate rattling ( I have heard this on several EB motors not just the Raptor), seems to be a flaw in the design. Nothing to worry from what I have seen and been told just a bit annoying. The EB that Ford uses isn't the only motor that has this if that makes you feel any better. The sun roof squeaking, try using a di-electric grease on the rails after you clean them up. I haven't done this to my raptor but had to do it on my previous F250. Seemed to help a lot. Also you might want to try a seal grease (silicone based). It will help tighten the seal and not squeak. I use this on my convertibles to keep the top seals from making noise since I don't drive them much. Also use on my older cars to keep the door seals from drying out.
I definitely wouldn't go the route that Jake went if you don't like squeaks and rattles. He will be talking shit about his EWE in about a year when it is worse that his Raptor. Neighbor has one and we can hear him coming from way down the street from the brake squeal that Dodge can't seem to fix and the numerous other issues he complains about. He regrets buying his and he has only had it for about 9 months.
