How do I check port alignment between intake and heads

Tape your intake gaskets to the heads after heads are torqued down with the head gasket. Line gasket up to intake ports. This assumes heads are port matched to intake gaskets.

Bolt you intake down and torque to specs.

Now trace the intake gasket with a pencil or sharpie along top of intake.

Remove intake and intake gaskets. Tape intake gaskets to intake manifolds aligning with the trace mark you made when everything was bolted together.

Port match intake to intake gasket.