As far as "leaving them on the hook..." ...if something goes wrong; it's not really a "fix", you know? You would really have to be careful in how you'd approach that if something indeed did go wrong, because they can just say all day long, "You changed it from the factory specified setting..." and they can ride that to the grave. Just be careful with that attitude. Dealer work (I think, so SOCOMech or someone else, correct me if I am wrong) is only guaranteed and their responsibility if it's a warranty fix or something that doesn't alter the specifications of the vehicle as it left the factory.
There's plenty of horror stories about bad service at a dealer and somebody being told this and that, "it won't be covered", "we don't know anything about it", "the dealer can tell if you did this and they put you on a blacklist"....all kinds of stuff. Fact is, just because you take your truck in for an oil change, doesn't mean they're gonna hook up the scanner and look to see if you've gone past the 100mph limiter......techs don't go looking for stuff to screw you on. If a tech notices something that doesn't seem "right", it's because he's looking at that area as part of the concern you brought it in for. I myself was usually pretty good about vehicles that came in modified. I once did some warranty work on a pullied/intake/tuned Cobra, he had a problem with coolant getting on the belt.....I determined that it had nothing to do with the aftermarket pulley and took care of it. I didn't run and tell, put him on a "blacklist" (what?!), I admired a nice car and fixed what was wrong. Now if a vehicle comes in with a modification to the suspension and it's pulling to one side, then I'd have to call it like I see it and say, "well it looks like the shocks have been re-adjusted and that will throw the alignment off".....and no, that won't be covered even within the under 12k mi. warranty alignment. So I guess all I'm trying to say is that it's not really true that anything other than stock will get you nowhere, but obvious changes in the area of concern must be taken into account. Otherwise, the proper diagnosis would be off and that wouldn't make the customer happy.....and that's a whole 'nother story, lol. Basically, you can have the dealer do the perch mod but don't expect a free warranty alignment. Why I had to go on a rant to get that across, I don't know, lol.
What's the purpose of modding the shocks? Do you do both front and rear, or front only?
The front shocks have a 3 settings that can change the height of the front end. The truck is set at the lowest setting from the factory. So when you here about the "perch mod" and "middle" and "top" perch or setting, that's what's being talked about.
http://www.fordraptorforum.com/f9/top-perch-fox-shocks-adjusting-your-shocks-level-raptor-248/