I've had the same issues with the coolant pump. One thing I needed to do was shorten the feed tube to the minimum needed (this reduces the weight of the coolant in the tube). I've also found that when the flow wimps out, stopping and starting the pump seems to restore the pressure. I was looking at replacing it with an immersion pump in a rubbermaid container as other have done, but couldn't find one here with a 220V motor that I could control with the stock wiring. I didn't want to mess around with any wiring so I've letting it be. In any case I don't let the mill run unattended so I can manage with it the way it is (for now).
I also have the tall column, but use a cast iron tilt table to raise my vise(s).