Managed to get them back in last night. Spent about an hour fumbling around with the first circuit of bearings then hit upon a trick and the remaining two circuits were done in about 10 minutes.

Only problem now is the ball nut feels a tad notchy at irregular intervals when turning. Its not binding tight just a moment of slight resistance then it free's up. At first I thought I'd gone and got a ball somewhere it shouldn't be so stripped it down again and took a more methodical approach. Cleaned everything again, separated the 48 bearings into 3 piles of 16 and carefully loaded them back in.

Still the same notchiness... hmm. This was a Strike CNC supplied ballnut/ballscrew and I can't say for sure if it wasn't like that before I spilled the bearings. Maybe I've knackered it up with playing around but I like to think Strike CNC, struck again!

EDIT: Seems to run smooth if you load the ballnut. Strange. Any thoughts?