Not had wheels painted and certain discs are on flat.

Any other ideas???

yep...your rotors are not as straight as they should be?

Have you physically checked them for runout? Are they fully floating? might have some tight bobbins (vicar)

Slow speed jerkiness as you describe - with brakes on? or off?

If only when brakes are on...then it is your braking system..and the common culprit is discs. If not, then the mating surfaces for the rotors is not flat etc.. you know what I mean.

Head bearings is a clunky ballache and very obvious. Forks are also pretty easy to check if you rock it on the brakes but forks or head bearings don't have the symptoms you mention.