400 BB build issues

You have a couple concerns - is the water pump definately good? I'd seen impellers on backwards and they don;t work that way. The Source housings are crap. Buying one because it's cheap and requires modification is like buying a steak at a restaurant for burger pricing and only expecting to have to cook it. With the starting and stopping there is a very real chance the camshaft is going to fail. I hope you have taken every precaution on that end of things.
My order of operation starts with "lose the Source pump & housing". Put on a factory housing and a Milodon water pump. The housings are not hard to get or expensive - I have several if you want one pay to ship it there and it's yours. The Source product has issues that they don't care to worry about. I use them for many things - cooling parts ain't any of them.
Add the Mr Gasket thermostat. Not a "new one" from the parts store. Get the Mr G one. There are differences and that one is a better part.
Add the fan shroud. They are there for a reason - and it's not to impede first start.
Put a hose on thje overflow tube at the neck, long enough to get it out of the slipstream.
Leave the cap off for break in and expect it to burp. I always have the hose there handy in case.