Kev, If the aftermarket ignition burned up, when you push the starter button, the starter should turn over the engine over but the plugs shouldn't fire. The starter circuit has NOTHING to do with the ignition directly. To turn the bike over, power is connected from your battery to the starter solenoid (relay) via a red cable connection from the battery to solenoid. The solenoid is connected to the starter by a heavy cable. The starter body contact to the frame provides ground for the circuit. A wire comes from your starter button so that when you push the starter button, it completes a circuit that provides switched DC voltage to the starter solenoid to trigger the solenoid (which is really just a relay) and the triggering shuts a gate in the solenoid that allows power across from the battery lug on the solenoid to the starter cable lug.
Frying the ignition module may have blown a fuse. Check them carefully because sometimes they look OK but are bad. You can use a multimeter in Ohms mode to check continuity... that is, touch the ends of the fuse with the probes and if the fused element is really burned, it will show no change in value.
The ignition module is powered by switched voltage that runs from your fuse box to your ignition switch over to your right hand switch gear and through the kill switch... or at least that is how it SHOULD be routed so that the kill switch would kill power to the ignition but whoever installed the unit may have powered it with a lead directly off the ignition switch. I don't know anything about your ignition but if you continue to have problems and the Newtronics company isn't there for support, you may want to consider a Dynatek ignition. I think they may make a Dyna S unit for your bike. The Dyna S doesn't have a "box"... the ignition is contained within what could be called the pickup coils. If you don't see your bike on their site
www.dynaonline.com, you should contact them as I suspect one of their models will fit. Also, if you decide to buy one,
www.z1enterprises.com carries the Dyna S at quite a bit less than the manufacturer sells them for and ships overseas.