If the length of a .WAV file (i.e., the duration of the recording) exceeds the stim duration allotted in the scenario file, will the recording keep playing while VAPP moves on to the next stimulus?

Yes.  Long sound stimuli will continue to play past the end of the visual stim that started them, for as long as necessary, and VAPP should let you do as many other visual stim while the sound is playing as you want. The only limitation is that these subsequent stimuli shouldn't have any sound (WAV) files of their own - you can't interrupt one sound with another.

Where do I find sound cards that will work with VAPP?

To find a distributor in your area for the Sound Blaster AWE 64 Gold and Sound Blaster AWE Value cards, see http://www.soundblaster.com/products/sbawe64value/
and click on the "Find a Retailer Near You" hyperlink.