2010 with JDM 30k engine just installed ... Rough idle Help :)

Just finishing installing a newer JDM engine into a 2010 Prius I picked up with a blown engine/rod. I started it up this weekend and it idles VERY rough. Did not let it run long. I changed the oil and it looks completely clean and engine looked like new when purchased. I used the intake, EGR etc from the new engine. Any recommendations on what to look for or try? I don't think it is a gasket issue, at least I hope not. Had a 2005 that has been indestructible and thought I would just upgrade to the 3 ... not sure now. Rest of car is perfect. Thanks!! John

 

Sometimes I amaze myself at the things I space out while trying to be meticulous... I noted that when I put the new engine in that I did not put a donut on the exhaust manifold flange so while it seated enough to not sound like a Harley, I am sure that has a lot to do with it. Will do that this week and update. Thanks guys.

 

Oil was clean and not milky. I just changed that as well. Will fix exhaust donut issue then go from there

 

Fast forward with all the Covid stuff going on and not needing a car as much I replaced the exhaust donut. Drove car a little. Got rough and shaky. OBD reader shows a P0403 code. Question, I opened up the EGR cover. Looks brand new but should I manually be able to open and close the valve by pushing and pulling on the stem? It is completely stuck. Thanks for your input! John