I'm not clear on what your setup changed from and to.

Do you have actually model #'s for the old and new pump(s)?

Also, did you have two pumps and then go to a single pump?

When the system starts off working but then flow rate decreases, what happens to the filter pressure?

If the manifold pressure is dropping while the filter pressure is increasing, the problem is likely with the filter. What type of filter do you have and have you backwashed/cleaned it recently?