I have a MAK-90 and a new Polytech barrel assembly.  I'm trying to de-ban the rifle by removing the current front sight tower and gas block and replacing them with the new tower and block.

Right now, I'm having trouble getting the pins holding the old pins out.  I just bought some PB Blaster but two hours of soaking didn't seem to help.  I'm thinking about milling out the centers of the pins (~3mm down) on both sides to relieve some pressure.  Is there any other good way to get these out?

Also, how should I get the new parts off the barrel?  They seem to be stuck even though they were soaked in WD-40 (now PB) for a night.

That's a pretty tough task to accomplish without buggering up your new parts.  Have you thought about just replacing your old barrel assembly with the Polytech?

I am in the same boat as you.  I threaded the muzzle on my MAK90 but it still looks goofy without a bayo lug, cleaning rod, and proper FSB.  For $80 for a Polytech barrel assembly the price can't be beat but i'm still trying to figure out how to remove the old barrel without having to remove the trunion from the receiver.

Are you hammering from left to right (right being the ejection port)? Heat the FSB it'll eventually release those pins.  I broke 3 punches trying but eventually got mine out.

I would have replaced the barrel but I do not think I have all the tools to do so.  Is there a very easy way to do so?  Additionally, the gas port would have to be drilled on the barrel (thus, I assume the gas black would have to be removed temporarily anyway).  I'd gladly replace the barrel if I could (or, I suppose, pay for someone else to do it),

I'd take the rifle apart as far as I could, leaving you with a barreled receiver.  Then I'd knock out the barrel pin as if I was doing a build, with a press or a BFH, then get the barrel out, again with a BFH or press. You'd have to get some kind of long rod to stick through the rear trunnion so you could push the barrel out.  Then I'd just press and pin the new barrel in. Reassemble and you're done.  I know a lot of this sounds pretty obvious, but I don't know what everybody's experience level is.  Doesn't take much tools, ideally, you'd want a 12-ton press (a ball-peen hammer can suffice in a pinch, but it's hard to do it like that) and some carriage bolts (for pressing the barrel pin out), a good table vice, and a long piece of pipe or similar for pressing out the barrel.  You'd want to secure pennies over the muzzle end of the new barrel when you press it in.  Also, you have to make sure everything is well supported or you could damage your rear sight block.  If you rebarrel, it would be a good idea to get or make some headspacing gauges, too.  

I do not have a 12-ton press.  I have read about a method using a blow-torch and a dry-ice/salt bath.  Does this work well?

I'd also have to pin the barrel, front sight and gas block.  I think I can easily do this but I do not know how to drill the gas port.

Quoted: I do not have a 12-ton press.  I have read about a method using a blow-torch and a dry-ice/salt bath.  Does this work well? I'd also have to pin the barrel, front sight and gas block.  I think I can easily do this but I do not know how to drill the gas port.

Why would you need to drill the gas port anyway ?  I have heard of good results with using a propane torch to heat the trunnion and barrel pin for removal, along with freezing.  For installing a new barrel, you'd want to heat the trunnion and freeze the barrel.  Not sure what the purpose of a salt bath would be.  Yeah, the pins are relatively easy.  

Dry ice/alcohol... more surface area covered and it gets colder...

The barrel assembly came with all the parts un-pinned and the gas port un-drilled.  That's just how they sell it.