With all due respect to any of you who have achieved some success with performing surgery on the rubber and weather stripping, Yes if those areas are damage then it would be Necessary to go in there and remove the damaged materials. If it worked for you, Great.
When I try to fix something I start from the original manufacturers starting point as built. So i try and see how it was supposed to be Before we started having problems. If the windows were consistently causing binding problems I'm sure Isuzu would have made a fix before they left the assembly line just like they did with the terrible '99 engine problems.
If you were replacing the body side cladding and the holes didn't match up you could "fix' it by drilling new holes. But that isn't the way it was supposed to be. So that's why I said all the cutting and chopping were "unnecessary" IF it can be done correctly.
But for anyone in a pinch I guess any "fix" is better than driving around in inclement weather with the windows jammed in the down position.