so I recently put on a bigger fork on my enduro, I've noticed I've had a good bit of brake rub, I have done every adjustment I can think of (I'm sure there are many ways I don't know about) including removing pads and pushing the cylinders back in the caliper body, loosening the caliper holding the brakes on and tightening it back, trying to move the caliper into the best place by sight, etc. It almost seems I can't get the caliper far enough over to fit, but I have a feeling it could be cylinder being worn out possibly? not quite sure exactly what it is, they are hayes brakes if that makes any difference. any suggestions would be awesome!

spin it slowly and listen to it. is it constantly rubbing or just a certain spot on the rotor? if it's just a certain spot on the rotor, it may be warped a tiny bit. have you rode it yet? maybe it'll wear the pads down that tiny microfraction and it'll clear?

Does your new fork have post or IS mounts? If it's IS, make sure the mounting bosses are faced: i.e. - there is a machined bare metal face for the adapter to bolt to. The powder coating on fork lowers is usually pretty thick and can throw off how your caliper adapter mounts to the fork. You can 'face' it by hand yourself with an X-acto knife, a steady hand and a light touch.

"It almost seems I can't get the caliper far enough over to fit"
"Over" in which direction?
On a new build of mine my caliper and rotor would not quite line up right, so I shimmed the rotor outboard to where the caliper wanted to sit and all is well with mine. YMMV