Scott: 
Good to hear you are making this move. You could, and don't take this in the wrong manner, inform your clients that you are taking their orders by e-mail only-( I guess you could make some exceptions, but most companies have made the transition to the INTERNET by now, how else could they get their loan docs?)
Fax docs have the reduced resolution of 72-96 DPI which explains why a faxed  doc looks so bad. E-mail can be almost anything you want, and since I know you use paperport, as I do, I choose to print at 600 DPI and in the max format. I keep one copy in max and another in whatever the client requires. Doing this provides for a back up copy with no additional effort. I keep a "client" folder by month and year as well as similar "sent" folder.

Best of luck with these internet e-fax programs- I have a friend that still uses them- he says there are wide differences between them also , he now uses "pack e tels fax service"  , he used to use "e-fax" but was too expensive-(like $17/month).

Steve Meinecke