...When I asked this question while installing the first set of rear Bilstein 5125's, I don't remember there being this much discussion.
Its been almost two weeks since putting these new shocks on (boot down, opposite way from the first time), and I'm not noticing any immediate differences in how the KK rides. When I started to install this 2nd set, I ended up only finding enough time to do the left rear and installed it boot up. Only a few days later I got around to swapping the right side. I inspected my install of the left, and found the boot
FULL of dirty water - thus prompting me to switch the left side and install them both boot down.
Doesn't make sense now to me though, why a factory install would be any different? Even with boots removed, wouldn't the "laws of gravity" allow for foreign particles to work their way into the shock if they are installed boot up? Have you seen how much dirt and grit gets trapped on top of your suspension during/after wheeling? I do a pretty thorough job of cleaning under there, but I still find dirt on top of dirt whenever I remove the wheels. I think my skid plates lose about 20 lbs. whenever they come off!
Maybe I'm thinking about this too hard, but I guess I'd just like to know the "science" behind why we do things the way we do.