I didn't use the template that was posted. I bought my entire window set from Brothers Trucks when it was on sale a few years ago. I think you should be OK as I've never read anyone having any problems. On mine the seal is great and wind noise minimal.
The pic below is a mock up window to use instead of the glass for "roughing it in". Made of about the same thickness as the glass. Just need to put a couple holes in it for "handles" or something to grab on to. This is not my idea~ I take no credit for it
dne'