I can hear a difference in left/right but it does not entirely separate them. I know that you have posted this problem, but has it cut down on the benefits you recieve? Acutally, I have noticed no difference. At least with Delta meditation.
Now, if I were listening to a paraliminal in a traditional fashion, I'd certainly want the stereo effect--just for listening pleasure though.
An amusing note: I sampled the Natural Brilliance Generator for use in delta mediation....
and guess what? You know those portions where Paul vocalizes all of the negative sayings of our inner voice and balances them with positive, empowering replacements? Well, all the negative sayings are loud and clear, and the positive sayings are barely audible!!! ..not the effect I was looking for.
Believe it or not, I've been having much much better results by simply listening to Side A of the natural brilliance generator as I go to sleep (with delta), and then listening to Side B before I get up.
You talk about Cool Edit Pro and 2000. As you already know, one is extremely expensive and the other is not.
Zamolxe, The Master of Binaural Beats has taken me under his wing and is training me in the art of brainwave manipulation. He kindly provided this link on the bwgen yahoogroup:
http://newton.hanyang.ac.kr/~astrojy/down.html
And the first person to give me a lecture on piracy gets a nuggie! 
Is Pro that much better than 2000?
Not sure there. Though, for the purposes of brainwave manipulation, my intuition is that there is NO difference. Both contain the 'Brainwave Synchronization' option.
Does this program create higher quality mp3's and have true stereo effect, or am I wishing for something that can't happen.
Actually, it only does waves 'as is'. You'll have to save it as a wave and convert it to .mp3 via any number of converters. What were you intending on creating? Rather, how? If you're looking to make one big .mp3 file... it'll take a little creativity synchronize it all.
Another question that I have is that I am wondering if the Mind machine is needed to reach delta, or if good headphones and BwGen sounds encoded to the portable mp3 player are good enough.
130 bucks for an Orion or 200 bucks for a Proteus is a lot to pay for just a pair of audiostrobe goggles. I think they help enormously. But if I knew then what I know now, I probably wouldn't have purchased the mind machine. While it is helpful... I just don't get my money's worth out of it.
I also have problems falling asleep with my headphones on...they are very large and I like to sleep on my side. Do you know of any high quality headphones that are thin enough to sleep on your side.
You must go down in the spirit of a meditation. If you lay down with the intention to sleep... you're likely to just go to sleep. If you treat it as a meditation, you'll go the distance with the whole 60-90-120 or whatever minutes. If you plan on sleeping afterwards, just take the headphones off and roll over when you come to. If you plan on doing an insane anti-sleep regimen, you won't be sleeping. In the latter case, it is paramount to have a VERY loud alarm and a bright light you can turn on within arm's reach--perhaps some rousing music as well.
I realize that you are a busy person
I live to serve. 
- - -
Pragmatism in all things.
[This message has been edited by Brian649 (edited February 18, 2001).]