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I am curious as to why you are using vacuum filtration. It is much more effective to push the wine through the filter. I am an industrial chemist and I very rarely see a vacuum filtration system. Try putting your filter after the pump and you will see much better performance and you will never have this problem. You do need to monitor differential pressure so as to not exceed the recommendation of the media supplier (just like a pool filter). Most filtration systems for small systems don't have a differential pressure gauge, so just make sure your standard pressure gauge is placed on the inlet side of the filter. An increase in pressure indicates clogging and reduced flow. A sudden drop in pressure indicates a hole in the media or "blow-by" around the gaskets. Since your tubing is most likely very short after the filter, you can assume outlet pressure is equal to atmospheric pressure and therefore, is the same as differential pressure.
To answer some of your questions - vacuum would mainly only be used for wine because you want as little contact with Oxygen, it does not come in contact with any impellers or airrates the wine using a vacuum system.It can also fill bottles very easily and very little maintanice and cleanup is a snap also.
The typical filters should be able to filter 60 gallons plus (all depending on your clarity ) and if you notice that the vacuum is increasing and the flow has slowed down - I would come to the conclusion that the filter is partially plugged