So you changed the plugs _then_ the misfire started? Or they were happening before and you tried changing plugs?
The TJ radiators are known to self-destruct at some point, doesn't seem to matter how you treat it. Some of the long-life antifreezes leave bad-looking colored stuff.
I have no idea why they want to replace the alternator. If it were me, I would change out the radiator, and probably change the water pump, thermostat, and heater hose outlet that goes to the pump, just since I had it torn down. You shouldn't _have_ to do those just because the radiator cracked though. Also, you can't rebuild these radiators in any fashion, so I would go for a well-made aftermarket one rather than an OEM-style.