I really don’t believe that shift rod connector is causing the issue, but anything is possible. Like others have said, remove the other bolt also and see if that helps.
I’m hoping the driveshaft is not stuck into the crankshaft…
How many bolts hold this gearcase in place? 5 or 7? There is the one through bolt towards the rear, was that a bolt that you removed, or a stud with a nut on it? If it is a stud, salt may have built up around the stud jamming it into the exhaust housing, preventing you from removing the gearcase.
