Bubbles can and do cause problems with chillers...
You need a pump for the chiller that will meet the flow requirements; that will meet the listed duty cycle for the chiller, and tank size, temperture pull down, design of the chiller, etc etc etc. This information is usually published in the instructions for the chiller, as a range with a little bit of flexibility. This makes arbitrary pump selection a bad idea.
Another consideration, in terms of the mag 350, by the time it is all plumbed in it is not going to flow anywhere near 350gph, if you have seen that number associatied with the chiller you have.