The TR-140 filter comes in residential and commercial models. The commercial models come in a 2” glued fitting and a 3” flanged fitting model. 3” PVC has a cross section that is 2.25 times the size of 2”, so if you have 3” running to 2 x 2” filters you have a restriction by default before you ever get “inside” the filter. Bypassing the filter (the recirculate position) at the multiport valve won’t eliminate that because the valve itself becomes the restriction.
I believe the pump specs a 2.5” inlet on it, which means running 2” PVC (or even 2.5” in this case) from the pump to the filter bank could also increase the head and slow the flow down. Your vendor likely would have already discovered this instead of trying to sell you a new filter.
How is the flow rate being measured and how often?