The two-week rule is intended to give your system adequate time to adjust to the changes. During those two weeks, stones will tend to "move forward" in your system, making them available to be flushed out. If you have obvious symptoms, you will know that stones have "moved forward" when some of the symptoms return.
If you feel up to doing another flush, then do it. It's your call, and you're the only one who knows whether or not you're up to it. Many folks have done them weekly for awhile. Some have even done double-ups, where they do two flushes in a row (two nights in a row).
But until you're used to it and know what you can take, the two-week rule is best.