Ive been running MSD T/L for 10+ years on various ski's from old 550 kawasaki's to the latest superjets and A/M hulls and from analogue to single channel digital and the current multi channel digital...Never have I run them in a box and in that time I have had 2 brains poop themselves, one analogue that was probably close to 20yrs old and one brand new 43251 multi channel that was sent back and confirmed faulty by MSD and replaced under warrenty.
If wired correctly, with weather pack or deutsch connectors on EVERYTHING, dont use a switch (waterproof or not) for your on/off, use a single pin weatherpack as your switch, use only the MSD connectors supplied in the kit or dual wall heatshrink on all your other connections, and use a little dielectric if you feel the need and make sure absolutely NOTHING can short out, you should have years of trouble free service from your MSD T/L in salt water.
Make sure you wash it down with a little fresh water when you get back and cover the whole setup with CRC, Inox, WD40 or whatever your favourite flavour is, then go have a beer and relax knowing it will be ready to go when you push the start button next time. The biggest killer i've seen with MSD's is poor wiring and shorts. (which usually come about from the poor wiring!)