I'm going to try and answer all your questions from your first post.
LauraB1) Will a CB affiliate who sends someone to that CB pitch page get the sale credited to them now that the button code has changed? In other words, does their ID get passed to EJ? I'm guessing it does, but I want to make sure I understand.
If the purchase button is an E-junkie button then yes the affiliate will be credited in our system.
LauraB2) In an old thread here at EJ, you said, "E-junkie's Affiliate programs cannot work with ClickBank checkout payment." I'm assuming this would not be an issue for me, as any of my EJ affiliates would be sending buyers to my original sales page with the PayPal and Google Checkout buttons, and my CB affiliates would be sending them to the pitch page I created for CB. Is that true?
Yes, that is true, your affiliates that send your buyers to your E-junkie sales page will still be credited.
LauraB3) Is it actually necessary for me to have two sales pages?
If you want to have a setup where you are using both E-junkie's cart/buy now buttons and buttons that ClickBank offers to sale products, then yes your would. However, since E-junkie works with ClickBank you do not need to.
LauraB4) I ran a test transaction through ClickBank and it went fine, but because I inadvertently had one of my EJ affiliates' cookies in my browser from a while back, the e-mail shows he got credited for the sale. Since it wasn't a real transaction, did he really get credited?
If it was a test transaction and no money was actually collected then the affiliate should not be credited.
LauraB5) Regarding the two affiliate programs: This is probably a dumb question, but are they totally separate? By that I mean, I have my EJ program set up with a 55% commission and my CB program set up with 50% (to offset CB's higher fees). Is there any reason I can't do that?.
You can have it setup this way. The one thing you want to avoid is an affiliate that is setup in each system, as each system would then record a sale for that affiliate.