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Patrick, the filter should be on the pump output side. On a vertical mount, I've always run the pressure side to the top.
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With pressure to the top, the column of air (if any) will be compressed - I don't think you'll get pressure any faster.
I always do it the other way - oil in at the bottom. That way it is self-purging and the air is forced out the top.
Not that you should have any air in the system, but......
I also run an Accusump.