So It lookes I only ended up answering one of these QtP back in the day, I'll try my best to answer the others even as we know how S3 worked out!

1) Is Pam's toned down behavior towards Jim more conscious or subconscious? Is this behavior change an attribute of FNB or Old Pam?
Definitely conscious, and at first I thought it was attributed to Old Pam, but now I think it's more FNB. When I think back to when Katy was around, Pam never really retreated to toned down behavior, she still cooked up pranks with him and participated in innocent flirting at work, and when Katy was around, Pam openly mocked her. Now Katy and Karen are completely different, and the situations are very different, but I still think Pam is being more mature in dealing with Jim and Karen, she's not really backing down as much as she's decided to let Jim reach out to her, and to react accordingly when it happens.

2) Should we be worried that Pam will become overly optimistic again? How should she proceed with Jim? (What's her next move?)
Well as we know now, yes, we definitely should have been worried about her getting too optimistic. She played things well until Ben Franklin, and while it certainly wasn't her fault that she slammed up against Jim's re-established wall and then had that talk with Karen, she was so unprepared that it sent her reeling, so if I could go back in time and give Pam advice I would warn her it would seem hard and impossible but don't give up.

3) Should Pam play a prank on Jim to even up the score? Would this hurt or help JAM's reconnection? What about a prank on someone else?
Though it didn't make the cut, Pam turning the tables on Jim in that deleted scene was pretty perfect, and would have definitely made some interesting analysis!

4) Now that Pam knows Jim is seeing Karen, how careful should Pam be about forging a friendship with her? Will a friendship with Karen effect her chances with Jim? What about any moral implications that might plague Pam's thoughts?
I would have loved for the scenario to be different so that Karen and Pam could have been friends, the small glimpses of friendship we got were great and wow did Pam ever need a good girlfriend, that seemed like half her problem throughout the entire show!
That said, had Karen and Pam become good friends, the JAM would have been delayed (if it happened at all) since Pam would have taken extra care not interfere with Karen and Jim, the beach confession would have not happened, Jim quite possibly would have gone to New York and things would have been different for sure!

5) Is it appropriate for Pam to get Jim Christmas present? If so, what should she get him?
It's really hard to imagine a more perfect gift than the one she gave in Benihana ;-)