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Blinking CEL should set P030x where x is misfireing cylinder
the blinking CEL means
the ECM thinks you have a cat killing misfire , stop driving right now .
so
there should be a P030X DTC where X is the number of the misfiring cylinder .
try to get your car to someone with
a scan tool with
GM Enhanced software ,
i believe the scan tool you are using is not up to the challenge.
the other (unlikely) possibility may be
CKP CMP alignment or more likely in compatibility because the replacement engine has a different crankshaft or camshaft wheel / teeth set than the original engine .
IF hot intake vacuum is 20 to 21" then there is no Cam Crank misalignment error , what is your intake vacuum ?
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