The reason you get less pressure in your filter when you close one of the two suction valves, is that you are increasing the suction head and thus reducing flow in the system. Less GPM on the return side means less PSI on your filter guage. If you had a vacuum guage on the suction side, you would see this rise when shutting off the valve. This is why to get an accurate head reading, you need both the filter PSI and suction inches mercury. Calculating total head from just the PSI reading is a very rough estimate and can lead to errors for this type of special situation.
Increasing the head on the return side has a similar effect on the suction (less suction).
The vacuum cleaner should not be an issue as you are going to a stronger pump. You may need to balance the valves so you do not have too much suction on the cleaner.
At 50 feet of head, the new pump will be at about 60 GPM so you will probably be ok. My guess is that your head loss will increase to maybe 55 feet of head because the pump is stronger so you should be under 60 GPM and not need to restrict the flow at all for the filter.
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