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FWIW, on a mono tube nitrogen charged shock like the 5100 their orientation does not effect their operation.
As mentioned Bilstein's answer is to mount them so that the decal on them with the writing is facing the right way so you can read it.
Mounting boot down is more of a longevity thing as it doesn't allow dirt, grime, salt, water, etc.... to collect around the shaft seal. If they are boot/shaft up the body acts somewhat like a shelf and allows stuff to sit around the seal. But, on some shocks you have no choice but to mount them boot up. The boot keeps most stuff from ever getting in around the shaft anyway.
As for rears....if you were to swap the sleeve out of the bushing you could flip them.
The pin up top is a larger diameter than the bolt that goes through the rears. There is a sleeve that goes in the bushing on the bottom for the bolt....no sleeve up top since it won't fit.
Jerid, you will find, as I did, most folks prefer the Bilstiens. I put mine on about a month ago and man what a difference. Mine didn't have any instructions with them so I put them all boots down. I agree that this will possibly help with longevity. I also agree that it more than likely doesn't make a difference so whatever you prefer.
it is possible to install the rear shocks with boots up on the 5100's. That's how mine is front and rear. Just looking at it.....it's wayyyy too close to the exhaust to do boot-down without melting it.