On stopping, shut off the fuel is probably the quickest access. Yes, when you pull the cap off the plug, Mercury prides themselves in a 40,000 volt pulse in just microseconds! No spark plug gap to stop it and you get the whole enchalada!
The key switch in the OFF position, grounds the black/yellow wire coming in on your remote wiring harness which kills the triggers and stops the engine.. Has nothing to do with L&S....just a freak timing of a different problem (see explanation below).
The cam roller has a white line as does the cam....your alignment marks....gotta rotate the roller to get it's line horizontal, and the idle stop screw presets the idle with the butterflies closed, a timing adjustment at around TDC degrees.
The next figure in the manual is to get the cam off the cam roller....don't want it touching, reason for the .005 gap. What this does is ensures that your throttle arm, when pushed all the way back as in the idle position, will stop as a function of the idle stop screw, and not the pressure of the butterflies in the carb pressing against the venturi case......did you remember to lock adjusting screw you loosened for that alignment.
The last step in the L&S is setting WOT stop screw which means the engine throttle/timing (20*+ BTDC....which is screaming fast) is at WOT and you have no linkage hooked back up at this time so the remote throttle is useless. Going to bet that's what happened.....you started in the WOT throttle position.
On the key wouldn't stop it problem, the engine (like happened to me once) probably went into pre-ignition overrun (ignites the fuel mixture with preignition sparks in the cylinder) which I had happen to me on one occasion doing the same thing....fiddling with timing. The Merc OEM 7k tack was on the peg....rpms out of sight, engine screaming, sacred the bageebies out of me....took a second or two to get my XXXX together. I had the same problem in that I couldn't shut down the engine. I squeezed the fuel line and got it to stop.
Once I got my wits together, I went back through things and got the engine started and it's still running like a top....it's usual self, with nothing else changed as a result of the instance. Was really surprised is survived that and didn't have problems later on.
So, before you go off and try to fix what probably isn't broken, put things back together, your linkage back on from your remote and go through your normal starting procedure. Hopefully other than setting your idle, it should do for you as expected.
After you get it on the water and running, then setup up your final 675 +/- 50 rpm in the water, F gear idle throttle position, boat moving using the idle stop knurled screw and locking nut.