Not a Gen 2 expert but if the shift shaft was not aligned with the foot when going together, it can bend the shaft. Not saying it did, but this has happened to others. This can also put excessive pressure on the shift crank. Could be it was in a bind until moved around to free it up.
The shaft was fine, just not lined up properly the first time I put it back together, therefore no reverse... Didn't start the boat till both forward and reverse gears were regained, so no damage should have occurred.
Just wondering about the initial tight (rubbery) shifter... Need to put her in the water for a test drive...