Okay this could be a lot of issue .
If you had the manifold off did you connect the vacuum lines at the back ,
was the manifold gaskets (blue rubber gasket ) replaced could be sucking in air ,
Was the No, 1 coil connected correctly this is the coil under the manifold back row
Was the plugs check (Gap) is the coil bad .
You should first remove the manifold again remove the No1 coil and remove the plug .
from the front row remove coil and plug and fit the No.1 plug and coil in it place , now the good coil and spark plug fit in the bad cylinder No.1 .
Replace the manifold clear codes , start and run engine, if still misfiring check for codes if the code changes to another cylinder to where you put the coil and plug from No.1 then we know we have a bad coil or plug .
If the misfire is still on No.1 then we have a problem with this cylinder .compression or bad injector .
Hopefully not . if misfire moved then check the coil swap over with one of the other on the front row (quick work)
clear codes run engine recheck for codes , if the code changes with the coil replace the coil if code stays the same replace the bad plug .
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