If you're brave, you might try using a sanding disk, but you risk breaking the glass. Ask the glass shop what they'd use as far as grit size. They may not charge you that much to fix it up.
You might double check the fit of the channel in the door frame, just in case. But comparing with the original glass probably confirms the incorrect size of the replacement.
I bought glass from Jim Carter as well, and had no issues with anything except the passenger side wing window, which doesn't reach the gasket at the top when closed by about 1/8", so it leaks when it rains. That might be an issue with my installation though as the driver's side fits just fine. I plan on replacing that wing vent window with one that's a touch larger.
