I have a Perkins 107 and have noticed similar symptoms to what you describe. I am no expert but for what it's worth: I left the the cap off the header tank until the thermostat opens, like that you can see the when the coolant is circulating. Shut down the engine or replace the cap pretty quickly after this happens or else the coolant will start spurting out.
I also found that there is a small bolt on top of my heat exchanger that allows you to bleed air from the system. Even after doing these things I have found the hoses going to the water heater don't get hot, least not straight away, until I increase the revs for a short while, thirty seconds or so, then I can feel the hoses get hot. I'm cleaning the coolant system so have drained the water quite a few times. Made the mistake of adding a chemical to aid cleaning, it ate my aluminum water heater, so I'm flushing the system repeatedly with water before I hook up the hoses to the new water heater. Only other thing I can tell you is to run the engine in gear, as it likes to have a load put on it, as well as causes all the fluids to circulate. One last thing, (going on the premise that the only stupid question is the one you didn't ask) can't imagine that the new water
pump you put on is faulty, or running the wrong way, put at this point in your "discovery", it's good to put all the cards on the table.
Good Luck
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