I have also done Marine Goop installs (twice) and not had any issues either time.
The second time I used some foam from a walmart camping/sleeping bag pad (about $5) and made a cut out to fit the transducer. I glued this down first and at that point there's the option to fill the cut out with vaseline and press fit the transducer for a temporary install, or fill the cut out with marine goop, roll the transducer and press in well (as mentioned) to remove bubbles, and you should be good to go. I chose to do use the goop again.
Not sure about the 3M glue. I'm assuming it's clear? I have used 3m 5200 for boat repair in the past, it was black, and very strong. I cannot recall how hard it cured, but I do know the Marine Goop dries somewhat rubbery and flexible- good if any future changes or a redo is neccesary.
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