Jeremy, is this a replacement window you installed, and you replaced something with a Wenco wood window? Casement or double-hung?
If you have replaced old single glaze windows, you should no longer need the storm windows over the opening. I would not install them.
The installtion is suspect. Rather than moving the jambs out to fit the openings, it would be better to use shims between the new window and the rough frame, then insulate in the gap. If you have stretched the side casings to fit the openings to the point that the window stops don't work properly, I would reinstall with shims and spacers.
I may not understand what type of windows you are installing, or the problem you describe. If so, please clarify. Good to see you back rebuilding Chicago.