I also swapped over the water temp sensor from the old manifold and found the PCV valve too. The latter is a one way valve that allows air to be drawn into the manifold, but not out - it is used to create a vacuum for the brake servo.
Next job - re-fit the water pump with new gasket. A nice simple job, clean the bolt threads, fail to find the missing bolt, order new one from ebay, apply sealant to gasket, fit water pump and tighten bolts to specified torque - simple. The last bolt, on the last turn when CRACK, and cracked the casing. See below. I guess torque wrenches are not that accurate and the casing was weak at that point. Not worth risking the leak so another £39 on Ebay for a replacement pump.
Summary: an expensive and frustrating week.... Ah, but that's what kit cars are all about - ups and downs, achievements and sorrows, and all have their cost.
Next job on the list is to re-fit the Flywheel, Clutch, and starter.