What water neck are you using? I had the same issue on my engine with a cheap off brand, after three failed attempts I ended up buying a Ford Motorcraft neck and it solved all my problems. Another tip I received was using a few dabs of RTV on the T-stat to hold it in place so it will not move when attaching the neck to the manifold. Your setup is looking awesome, those stack injection setups look fantastic.
Here is the water neck I ended up purchasing:
https://www.cjponyparts.com/ford-rac...CABEgIo3_D_BwE