Using bit fields instead of individual scalars to represent boolean data will save you a measure of memory consumption, but the same architecture that is getting you into trouble now will get you into trouble in the future as your needs grow again.

I consider moving from individual scalars to bit fields a micro-optimization. But you're not micro-challenged; you've got a design issue.

It may be easier to deal with all this than you think. Perhaps you could create helper classes to handle the behind-the-scenes storage and retrieval so that the majority of your script can remain unchanged. ...without seeing the details my suggestion has to be vague.