I'm guessing you've sorted the problem by now Gary, I've only recently joined the forum so have only just seen your post. I have just fitted the Thorspark unit on my 59 A10 GF but mine is auto a/r so I used one of the other notches. As far as I can tell though, you have done it correctly, the manual a/r utilises the long slot and then the unit is held in by the cap. You will probably need to fit the spacer supplied in the kit to get the required clearance.
I've only recently bought the bike but I was having a lot of trouble with the mag, probably a lot was due to a worn cam ring but I made the decision to go electronic. A lot of the reason for that choice was because of the timescale for getting the mag reconditioned. It's early days but I have to say I don't regret my decision, glorious fat blue sparks, first kick starting, hot or cold and lovely even tickover. Also, it can be reverted back to mag if so desired with no damage done.