Replace the original castle nut that retains the water pump pulley with the "nyloc" version, now sold by Moss (TD catalog, page 10, item #8). Tighten it down until the pulley is firmly seated on the pump shaft. I also didn't get my pulley nut tightened enough on an earlier rebuild, and it did start to wobble over time. The nyloc, properly tightened, has solved it.
Removing the thermostat sounds like a good idea for increased flow, but some say the coolant actually needs to slow down in the cylinder head to absorb more heat before returning to the radiator. The sole purpose of the thermostat is to allow the engine to warm up to it's design operating temperature quickly. Once it's open, it has no further effect on the cooling capacity of the system.
The thermostat by-pass loop, without the old-style thermostat sleeve installed, will allow hot coolant to "short-circuit" the radiator, returning hot coolant to the water pump and block. If you've pulled the sleeve, also block that bypass hose - a 3/4" PVC line plug will fit the hose interior nicely.