So I bought and Aliengear Cloak Tuck 3.0 and... my side is burned to all hell.  I get so much chafing, not from the gun, but from the part of the holster that sticks up against the beaver tail.  The holster does not sit right against my body, very disappointingly.  It's so stiff that it won't conform to my frame, so even though the 3.0 has a nice soft backing, the pointed up part scratches against my skin from the side because it's not sitting flush against me.  I can't find a position to put the gun in where it's comfortable.  I've moved the clips around to my heart's content with no satisfactory solution.  Any ideas?  My pants have more than enough room to fit the gun, so that's not the issue(I actually went and bought pants too big for this reason).  Should I try another brand of holster or switch OWB?

Maybe put a layer of moleskin on the part of the holster that goes against your body?

I've had to do that with several holsters in the past.

Mine would irritate me if I wore it at the 3:00 position. I wear it at the 4-4:30 position, and it is not irritating with my Glock 19, or bodyguard 380.  
Some people wear their IWB holsters outside of their pants. They say it works just fine.

Do you wear an undershirt?

I wear undershirts all the time one to keep me cooler by not allowing sweat to evaporate off me as fast and also keeps my holsters from rubbing against my skin.  I wear Adidas nylon\spandex shirts that have a little stretch to them the UnderArmour version also works as well.

Op you don't mention it but are you wearing a belt designed to support a holster? If you are disregard... if you aren't then try finding one. A thicker belt with reinforcements designed to support a holster and firearm can make for a more comfortable CCW experience.

I have tried the 1.0 and 2.0 AG holsters and in the long run I was disappointed.

Why have a $1,100 pistol and such a cheap holster?  I would suggest you try THIS and never look back.

I have been carrying my EDC in a MTAC now for about 8 years and could not be happier.

I haven't tried the alien gear yet, but i will be soon so I've been doing a bit of reading. I have read that some people need a break in period for things to soften up and conform to the body.

Maybe try wearing it more and/or working that part of the holster to soften it up a bit.

That's BS if your talking about the 2.0 or 3.0 holsters with a synthetic backing, they do not break-in or conform to the body like leather.  I carried a Shield in a AG 2.0 for about 3 months and it never did any "breaking in", it still appeared perfectly flat with zero deformation when removed from the body.

Get a good leather backed IWB like a MTAC or Crossbreed and it will start visually conforming to your body within a week or so.

Where are you trying to wear the holster that you say your side is getting all scratched up?

Something like the MTAC is your answer.  I have several carry holsters but the two that get used 99% of the time are MTACs.  They are the most comfortable holsters I have used, no undershirt required.

Like I said, I don't have any experience with them, just reading reviews.

I am planning on getting the cloak tuck leather, but I'm going to see if it has any neoprene on it before I buy, I don't want any neoprene.

Cloak tuck leather

I have one of the AG holsters in a box somewhere never really given it a good carry to evaluate fully.  I think it does not break in well because of the metal liner sandwiched between the layers.  The reason I never gave mine a good carrying was I got it and shortly after switched to a WML and the holster does not use a light.

Why do all these people flock to metal lined holsters then complain they don't fit right?

I use an AG leather backed for my G21 and it was one of the most comfortable holsters I carried with. I won't buy the goofy 2.0 or 3.0 because they won't hold up as well or be as comfortable as leather, at least to me.