Soooo I think I've solved it!
I took the countershaft bolt off and it was pretty easy to get the front race of the bearing out- and at the same time I could see in to the inner race. All balls present and correct. Hmm- let's try main bearing. A faff to try and take it apart as I didn't have a socket long enough to undo the nut. This made me stop and think. I opened up the detent ball housing and this time actually took the balls out. All 3 were there BUT they were identical to the one I found.
So it seems that the ball was a detent ball lost when I got the gearbox overhauled- I guess they gave up trying to find it and fish it out.
SP3 you are the winner!
Thanks guys for your help!