Let's take this one step at a time. From what I gather, the audio is your major concern. Since analog audio isn't sufficient, then I think it's safe to assume that your LD player has digital audio out (either coax or optical). The Pro BOB supports digital I/O via both coax and optical.
How you capture is really the issue. Your best bet it to capture using the EZCapture utility. In the Settings dialog, on the Codec Settings tab, you can select the customize box. This allows you to change both the audio and video settings to meet your requirements. As DV doesn't use 44.1k audio, your best bet is to use MJPEG or DivX (change the video settings to highest quality for either), and change the audio sample rate to 44.1k.
Unfortunately, my Pro BOB broke a while back, and I've never had it repaired, so I can't tell you if the digital I/O will be resampled at 44.1k or merely copied as it's already 44.1k.
But I hope this helps to answer some of your questions.