Curious if there were any blades missing from the old impeller? A broken blade will go downstream and cause a clog.
Time to start disconnecting hoses and see where you have flow or don't have flow. When you have a hose disconnected, an easy first check is to just blow into the hose. A clogged component will be apparent. A common clog site is the outlet elbow from the manifold.
I would remove the thermostat while you're doing this. Once things are flowing, you can always put it back (or not).
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