If you use workbench and other apps a lot, rather than just playing games, I would just buy a scandoubler/flicker fixer for it as its just the best option for AGA. 640x256 just doesn't cut it for anything but the earlier software, especially once you have become accustomed to using 640x512, as you have on your 4000. Not only does 640x512 give you a whole lot more room, but its actually a proper square (well near enough) image, where icons and everything else are displayed in proportion rather than stretched out.
If your sticking with the commodore monitor, perhaps it would be best to ditch os3.9 and go back to workbench 3.1 and its far more simple appearance thats better suited to lower resolutions.