After a bit of work on the 36v controller connections putting on matching connectors I now have the cyclamatic working with a 36v battery and controller. Will let you know if there is much of a difference after a few test runs.
Smoke normally means that you connected the battery the wrong way round. If you do that, it smokes the main capacitor. It can also vaporise the shunt, but if the shunt is still intact, it'll be only the capacitor, which is an easy repair.