Sounds like a radiator cap problem. It should only get the pressure specified on the cap. When it cools down, that pressure should diminish. Seems like it built up a lot of pressure, and when it cooled still had pressure residing in the system. Sounds like the cooling system needs a good cleaning and would do that first. The bubbles are concerning. After cleaning and refilling, I would run it with no cap and see if you can see bubbles coming up. Perhaps your new engine has a bad head gasket as well?