you may think its stupid, but on my boat I have the MSD box mounted to the back of the rear seat to keep it dry and I ran a bead of silicone around the gap where the dizzy cap and dizzy meet to keep it dry. I have a pretty much exposed flywheel and when I get a lil water back there it tosses it up and lands right on the top of it but so far it hasn't given me any issues yet. The old setup was kinda like the opti-spark mod for the Lt1 engine cars where you drill a lil hold in the side of the dizzy cap and stick a lil 1/8 vacuum hose in the side and run it to a manifold vacuum port and it keeps air running thru it at all times to keep it dry.
Also, Im pretty sure you could extend your wires for you MSD box and mount it somewhere under the nose of the boat, and it wouldnt effect how the engine runs due to the extra wire.
Just a few thoughts.
I don't think you're stupid...

Running vacuum to the dizzy is a huge no no..two reasons come to mind, one, electricity moves easier under a vacuum condition and while the 18-20 inches at idle don't seem like a lot, can cause some extreme cross talk or crossfiring of the cap electrodes.... two, if it will pull in air, it will also pull in water and not to mention oil....
That being said, if you mounted your MSD box to the rear of the seat, make sure the grounding wire is upgraded and connected properly (numero uno cause of box failures).
Get a dizzy diaper, mount the MSD box shiney side up (label up) and away from direct contact of heat and water (heat rises and the ribbed part of the box is the heat sync) and silicone on every electrical connection, I have become a real fan of dielectric silicones and greases.
These are just a few things that will keep things running during U-boat recon runs....

GT