I saw they had a 25fot racemaster or something with two 15" EFi-Mercs on it..(Got stolen or something I read..)
not that great difference from that and to your Phantom when it comes to the ballance-questons and so on is it?
I wouldn`t know since I have no experience with rigging two engines..
As for the cowlings, I think they will let the water in, mine does and it is in a decent shape all togheter, you could se it on the two lower bolts on the exhaust-chest..they were a little corroded.
You should post some pics of it when youre done, because that is going to be a special boat when it`s done. not to mention cool