dang that was hard to read man - break it up into sentences and paragraphs! My eyes got lost half way through it!
But yea - you can use the 3m adhesive to hold your carpet down. Spray the carpet and the deck and let it get tacky before you join them. If you've got a scrap piece of wood put it over it and lay concrete blocks or something heavy on it to keep pressure on it... that should stop any bubbling you might have come up.
Did it come from the dealer with that piece of wood on the transom?