Is there a program that will show the frequences in your audio clip? Just thinking such a program might help me sort out some troublesome noises/frequencies.

Not sure what software you are using. There are various plug-ins for this purpose. My Pro-tools, for example, has an Waves Psychoacoustic Analyzer that displays frequency spectrum in real time.

I'm using Vegas.

Izotope Ozone is a very nice mastering plugin that is available in a direct-x version, which shows up as a vegas plugin. It incidently has a frequency display monitor in its eq section (it is about 6 modules, the volume maximizer is awesome). izotope.com.

One quick way to find an offending freq is to pull up Vegas' native track eq, select one of the middle bands, narrow the spread, then grab the whatchacallit, you know, the little round dot with the number in it and boost it up all the way. Now, sweep it left and right until the bad freq is really emphasized. Fine tune it, now go to the numbers section in the lower right, and turn that +12db into a -6 or so, and see what it sounds like. This is much easier to do than to write about, just grab it an sweep it, with it boosted bad stuff really pops out.

If you're looking for a fast fourier transform kind of oscilloscope, something to show the frequency domain instead of the temporal domain, there's a number of freebie fft's available as VST plugins. here's one
http://mdsp.smartelectronix.com/ffttools/