My guess would be that a piece(s) of the old WP impellar is floating around in the system and intermittently clogging it up. If this is the case the remedy would be to give it a serious back flush until some pieces are found.
Dueling Duratecs
'95 SE V6 MTX 0 Mods
'04 Mazda6 S Wagon
'03 Kawasaki Z1000
But thus do I counsel you, my friends: distrust all in whom the impulse to punish is powerful!
Friedrich Nietzsche
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