Im supposed to run part 2 of Gatekeeper this Sunday , but real life has gotten in the way this week. Im currently reading it, bur am having a hard time wrapping my head around it. Can anyone out there help me streamline all the details , or someone give a synopsis of how your group went about it.

We're a mostly Edge group, but our doctor is FS and is the one the story is mostly for, he found the holocron.

Could the Whitescar syndicate be replaced with a branch of Black Sun?

It could be replaced without much problem, absolutely! The Whitescar syndicate is only a name, not referring to anything greater than itself.

I will also run chronicles of the gatekeeper (haven't read episode 2 yet) and i was wondering how can one incorporate credit rewards at the end of episode 1, does anyone have any idea?

I am currently reading episode 2 and i agree with bsmith23, this part of the adventure needs a flowchart, i will see if i can make one up.