I'm late to the party as usual here but it doesn't remove the "load" from the switch to have it on the ground side, it just removes the voltage from it as the "load" in the circuit (bulb, starter, computer, etc.) uses up the voltage before it gets there. Amperage though is the same throughout the circuit, power or ground side. Most vehicle manufacturers place switches on the ground side as the lower voltage reduces the very minor arcing across the contact points (where there isn't a transistor these days) caused by the additional voltage going through it and in theory making the switch last longer.
If removing the kill switch didn't solve the problem check for voltage loss across all the wires in the circuit. This is important, do it with the circuit operating. Set your meter to volts and connect it to each end of any wire you want to check. In your case each end of each black and red wire as well as across the kill switch contacts and alternator wire. On the large gauge wires going to the starter you'll have to disable the ignition system and measure it while cranking. I would pay special attention to the wire from the alternator (it might be too small for that span) and on this one the engine will have to be running, if it will run, if not while cranking will have to do. You should read very little voltage in any of these test, not more than 0.1-0.2 volts is ideal, if more than say a volt there's way too much resistance in the circuit or the wire is too small in diameter.
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