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SD WHALER,
I recently restored a 1989 22' outrage with whaler drive.
in my opinion, when boston whaler decided to close in the transom of our boats it was a bit of an after thought and the plumbing was poorly conceived.
As far as i can tell, the factory did the following:
-Filled in the splashwell with polyurethane foam and screwed a plastic cover over it. mine leaked and the foam was soaked
-At this new "floor level" they added a drain on each side that drained water from this area out into a void between the transom and the whaler drive. mine were poorly installed and had little to no sealant used. be sure to check this.
-They also added two drains that drain water from the main deck through to the aft area. again these are pvc and poorly installed with minimal sealant.
-They added two pvc rigging tubes to the upper part of the transom. check the seals!
It sounds like your outrage is set up similarly to the way the factory originally set it up.
for what its worth, here is what i did to mine:
-Re-installed the transom drains properly sealed with 5200
-Re-foamed and then glassed over the splashwell
-Glassed over the aft bulkhead drains and drilled new drain holes to allow water to go from the floor through drains in the aft corners into the rigging tunnels and then into the lowest point in the bilge.
-Installed a bilge pump at this lowest point
-Drilled and glassed in rigging tunnels from the aft area to the exinsting tunnels to get away from the cables, wires and hoses being exposed in the aft corners. now it is a much smoother run from the console to the motors
there are a mess of photos on the attached link. maybe its useful...
I hope this helps.
Cheers!
http://s96.photobucket.com/user/wdunl.../slideshow

(Fixed linked as requested. No problem)