i recently bought a used bow off someone (PSE Rogue X MF)
and i have a feeling that the bolts at the base of the limbs are not in sync. i have thought about tightening them all the way down and then backing them back out, but will i damage the rubber bushing that goes between the limb and the riser?

It should be safe to do this. Once you have them cranked down. Back them out at 1/4 of a turn a piece untill you reach your desired weight.

I measured mine. I'm not sure of that bow, but on my pse it says the limbs should never be cranked down past 3/8" from the riser. I took a 3/8 allen wrench and slipped it in there until both were exact, and went from there

Thanks for the replies everyone. i work in a machine shop. so what i wound up doing was taking a set of digital calipers and measuring from the limbs to the risers. the difference is about .01 of an inch. i feel this is close enough, but im not sure how close they have to be. what do yall think?

That should be sufficient enough to get an accurate draw weight.

You are measuring sort of the wrong thing. What you did you should do to start with them even, now set the weight to what you want. Now you should measure the tiller measuremeant (from teh string into to the limb pocket). This needs to be even top to bottom. If not, adjust one or the other SLIGHTLY to get them even.