The clutch switch is there to allow the electric starter to work when the neutral switch is telling the computer the transmission is in gear.
It doesn't try to kill the engine if it is or it is not engaged.
The sidestand switch on the other hand will kill all power to the engines running circuits if it is deployed.
In your case, since it doesn't exist it can't kill the engine but, if the former owner just cut off the wires there is a chance that the ends of the wires are touching one another. If they are, the computer will think the side stand is down and it will kill the engine.
The wire for the sidestand switch just plugs into a branch of the main wiring harness with a plastic connector.
This is located down in the area of the left rear engine mount. If it is still connected there, unplug it.
If he cut off the wires above the connector, make sure the ends of the wires cannot touch each other.
No. the rev limiter doesn't make any noise at all. It just kills the power to the engine if it senses the engine speed is running faster than it is supposed to.
As for loudness, remember, these big singles are low speed engines. They make most of their power below 4000 rpm so don't race the engine to high speeds.
The loudness is most likely just the sound of the engine working. Silence lower than the Federal limit is not designed into the exhaust system. (I think it is about 80 decibels).
As for misfiring, you should try changing your spark plug.
If the new spark plug comes with a screw on cap on top, remove it before you try to install the metal spark plug connector.