You can just disconnect the lines and leave it where it is. Only time a mechanical pump can cause you grief is when the diaphragm in it splits and dumps fuel or it leaks oil (or it is tired and isn't supplying a constant/adequate amount of fuel). You will need a fuel recirculation cannister if you use an electric pump on the Mikuni carb as it has an external accelerator enrichment pump (the cannister has a main fuel in, one out and another line for the accelerator pump). The other connection on the accel pump housing connects to the tank return line. As for the coil replace it with a new coil (either a direct OEM or a transformer type coil with the same OHM rating) and as long as the rest of your ignition components are good all you'll need to do is retune the engine. I would install the pump as close to the fuel tank as possible so it won't struggle to prime from empty and will be quieter (add a filter before the pump as well to protect it from junk going through it and wearing it out)

*looked at the ebay listing above, my opinion is you can buy better quality and quieter pumps for a few bucks more (a hint - look at the Mr Gasket pumps and then compare them to the Carbole brand. Notice anything?)