I have had a starting problem with my 90HP Mercury 4-stroke too. here are the facts:
1. About 120 hrs on the motor (2005) - 40 of them since Sept 1
2. Stopped the motor to watch the sunset and take photos, engine would not startup afterwards. No sound, no nothing
3. Nav lights worked fine - but I think were quite dim
4. Connected a batter charger while everything was connected. After appearing to charge for a brief time, used the remote trim up (on the Quicksilver console) and it operated briefly then quit.
5. Removed battery and put a charger on it overnight - didn't seem to be taking a charge (although now when I think about it it may've been charged - never tested it w/ a voltmeter
5. Replace the battery and no go. This time, not even the nav lights (and things that are normally on in the OFF position weren't there)
6. Inspected under the console - found a black wire with some melted insulation and bare spots. it's one of the wires coming from the ignition harness.
7. Ordered and installed replacement harness - and connected it across the deck of the boat (just to confirm that was it)
8. Still no go. Can't even use the cowl or remote trim up/down - as if there's no +12V power.
9. Fuses (all that I've found, anyway) - check fine. Several withing the starboard side's electrical panel - and one on the +12V connection at the battery. (there are two other connections in parallel - black wires with no apparent fusing).