Your car could be running better due to a problem(loose connection or defective wires) with the equipment you changed(maybe the new wires are just better). You are probably burning the fuel more completely in the cylinder now(hotter coil), less unspent gas. Makes for better gas mileage as well(probably not a great deal though).
As far as changing the boot on the wire, I seem to remember there being boots available that you could switch on there. You might wanna check with summit or whoever you bought the wires from...
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