Well, creamsteak, you've got a whole lot of fun in front of you. I only wish that the time travel supplement I've been writing was published already and available to you. Oh well, you'll just have to make do with friendly advice in the meantime.
My main question while reading all of this was: how are you setting up the campaign? The "hows" and "whys" the characters come to possess a phoenix gate/chrono-artifact/time-shifting pooper scooper will go far, I think, to answering alot of the core concerns. For example:
Perhaps the characters are bopping along happily at first level (you starting them at first level?) when suddenly they are swept into another place. Here, tall beings with flowing glyph-covered robes ushers them to a conference table. Several items on the table glow with a faint magical aura as head humanoid tells the PCs that they have been chosen to be the keepers of their timeline. This example assumes that the mystical time monitoring race (which could be a silver-skinned variant of elves for all it matters) is one which exists to keep records for some type of universal uber-deity. They "commission" appropriate persons in each of the multiverse's timelines with making certain that time traveling ne'er-do-wells don't screw with the timestream (vast changes do, after all, make record keeping rather cumbersome).
In any case, the PCs are provided with a brooch which monitors their own timeline (and no others in case they travel to another dimension) and emits a particular radiance indicating how close the focal change-point ocurred, a mirror with which to visually communicate with future selves (the mirror might also be the item which future assistance travels through--the aforementioned fireball launches from it, a beam strikes the person to whom knowledge is being imparted, etc.--just to look cool), and whatever else you think the campaign needs. Should each PC be granted one of every item? Up to you! Might make it more interesting that way.
As for the whle karma points/record keeping stuff, why not just make it an "eye for an eye" type system to keep things really simple. The mystical time humanoids mentioned above might warn the PCs that while they can get information and favors from their future selves, such requests backlash at unknown times with equal effect. I remember someone mentioning a +5 sword earlier in the thread. To illustrate this approach, say a PC does conjure this sword because it is needed to slay X monster. Fine and dandy, the beast is slain and the adventuring continues. Now, a few days/weeks/months afterward, the brooch(es) which warns of time tampering starts glowing. Is someone tampering with the timeline? The PCs can check in with the mystical time recorders--"Nope, no external changes. Must have been something you did, better be careful." What the brooch is warning of is that the +5 sword conjured however long ago is now back in play. When the next orc jumps from the shadows to attack, will it be wielding this dreaded sword? Probably, because the "retributive favor", once detected, will likely be imminent to properly stabilize the timeline. This becomes increasingly worrisome if, say, 15 orcs jumped from their ambush--which one has the +5 sword...do any of them?!
Hopefully I've not rambled on to much here and you can get some ideas.
Edit: And by carrying one of the magic temporal items (probably the brooch), they are immune to any changes in the timeline. Or, perhaps the mystical being can bestow a feat which works the same way. Depends on whether or not you want the possibility of the PCs not being immune to changes once and awhile (i.e. "oh no, I lost my temporal brooch!").
