The thing is with big singles is that you can get kickback from a number of different sources and it doesn't necessarily mean that there's a problem with the CDI. There is a starting "ritual" of making sure the piston is in the right place (just after tdc) before you start to kick - get it wrong and it may well kick back - or do nothing at all.

Even if you get it right but don't put enough "effort" into the kick it may well kick back (you have to put close to your whole body weight onto the kickstart - it's not so much a "kick" as an attempt to jump on top of it). If you open the throttle too much combined with a feeble kick it may well launch you into orbit when it kicks back.

Back in the days when you had mechanical bob weights to control ignition advance, having those stuck in the full advance position would pretty much guarantee a violent kickback but with CDI you'd have to be unlucky to have an electrical fault duplicate that. If the flywheel has been removed and put back slightly out of position that could cause it but it would have to be a pretty inept mechanic who managed to do that.

It does seem a little strange to me that the bike started in 2-3 kicks (probably about normal for my 600 singles) before the strip down but didn't have a spark after. The electrics shouldn't have been touched other than removing stuff and putting it back.