I have a 98 Accord Coupe LX. For a few months I knew my regulators were bad and finally replaced both sides.
After replacing both sides though (they needed it the spring was broken on both), my windows stop about a half inch from the top. Previous to replacing them, the Windows both rolled all the way up.
I have spent a while tinkering with it hoping to find some way to make adjustments but have not had luck.

Any advice?

 

Sounds like your regulators aren't positioned properly or the glass isn't in them properly. If you know the glass is properly seated in the regulator, search for whatever bolt lets you move the regulator up and down and see if any position causes the glass to go all the way up. Retighten the bolt(s) when you fight the right position. There is a video on YouTube that I saw before, and the guy shows that at least one of the holes in the door is slotted in such a way that the regulator can be positioned higher or lower. Good luck.