Uh, I think I know your problem. You should refill liquid from the fill tube, turn the pump on and off, get the bubbles out, and refill more liquid if necessary. I think you just don't have enough liquid in your system, I doubt you have a serious leak or anything.
You know what I do, I actual fill the entire thing with a funnel from the fill tube. DOESN't actually take that long, and isnt' hard at all. I have my wye splitter between the WB and the pump, which makes this a whole hell of a lot easier. The pump needs to be unattached for now, tho. Dump water w/ additives in until the liquid comes up to the top of the fill tube. Flick the tubes a little and you'll get mad bubbles from the liquid filling the inside of the pump. Once the liquid falls lower than the wye, repeat the process. Now, for the bubbles in the rest of the system, flip the pump upside down so liquid runs out of the pump, and the pump fills with air. "Guide" the air bubbles out the pump intake, and up to the wye splitter. Refill the fill tube to the back to the top every now and then. Once you've removed all the bubbles you can remove at the moment (the ones you can't get at are in the WB and the radiator), fire up the pump for just a sec. You'll get mad bubble movement immediately, but the trick is to gather the bubbles in the tube just before and just after the pump. That way, you can "guide" the bubbles out like before by moving and turning the pump around. Sounds like a hassle, but I assure you, its a lot neater than using a whole bucket.
I'll have new pictures of my revised MARK II later tonite, hopefully, and then hopefully what I said will make more sense.
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