Roo, probably a combination of both. the decks are not glassed down like most ribs so it is quite likely that rain water got in. It might be possible for the deck, normally above the water line, to get low enough for salt water to flood the deck before the huge reserve of bouyancy in the tubes starts to take effect as the tubes are clear of the water when a standard Pacific is lightly loaded. Especially as the stern drain letter boxes are at deck level and only a couple of inches above the water line.
I keep mine in the water during the summer and other than an occasional pump out if its been raining heavily never had a problem yet, until I met a yachtie
but thats another story.
However with a non standard boat the balance of the boat could be anyones guess. Since you are starting with a blank canvass you could return her to standard pacific layout or keep her with a close coupled stern drive. The easiest would be to put another volvo back in her, but was that a petrol volvo? people buy Pacifics because they are cheap diesel ribs, not sure if you could sell her easily with a big petrol volvo in her.