I'm not sure about Bordeux Inks, but some 3rd party inks are not compatible with OEM inks. If this is the case, then it's very possible that you have clogged the Damper and Printhead, you should have flushed the line then inserted your OEM cart.
If you have air in the line (which you should since you stated you ran out of ink), I would prime the line via a syringe, and not by 'pumping up". When you pump up your pumping up all ink lines, and wasting ink.
Once you have pulled ink thru, you still are not getting any yellow. I would check the Cap Top it could be in need of replacing, or cleaned at the very least.
I also agree with the other post concerning "Profiles". You will have color problems if your using Yellow OEM, and all other inks are bordeaux. Unless your making your own profiles in-house.
My $.02
GTSTech_1