Personally, I think there still needs to AT LEAST be an option for users to switch to the narrow version of the site, with the pop-up, etc. This isn't stemming from nostalgia, but practicality and professionalism.
Here are two alternative suggestions for how to go about implementing the old, classic version while keeping the new:
1) Have the narrow version as the default view. Why a narrow version? It is more professional, looks better for a lot of people (some would say more sophisticated), and works better for those with smaller screen resolutions (not that I have a small screen resolution). You could be losing a lot of potential visitors who are initially turned off by the unsophisticated look or something that won't fit on their screen. Most people visiting the site are browsers and won't care for a huge screen anyway. They're just here to view the content, not to be awed by wide-screen prowess (not that they would necessarily be awed anyway). In fact, many may prefer pop-ups because it is more practical with regards to site navigation.
2) If you keep the wide version as the default view, then I think the narrow version I speak of should rightfully be called the "Classic Version", and the new, wide version should be named something else (e.g. "Wide Version"). The option for pop-ups should be dealt with as an option via a checkbox (e.g. "Display Flash in Pop-up or on page?") on the new option page you made.
I wouldn't even suggest alternative #2 above if the wide layout isn't going to go global to begin with. If the wide version is only staying on the flash section or a select few sections, the site would seem even more unprofessional (and furthermore, inconsistent) than having the wide layout as a default but global view.
I have done a lot of designing in the past and it shouldn't be too hard to make the narrow version compatible with the wide version. Assuming that every table within the main borders is fluid, then all you need to do is fix the width of the main table being held by the main borders and the fluid tables should sort themselves out.