I'm in the process of replacing the old ball bearing headset for new taper roller bearings. Bottom outer race went in fine, top went in fine also. However, when I reassemble the completed yoke back together, I can't screw the nut back on as if the shaft isn't through enough to catch a thread. I've definitely got the bearings and seals the right way about too. Just something isn't quite right and I'll end up having to remove the new outer races, possibly damaging them in the process.

You have most likely checked all this but, assuming you have removed the cone (and maybe a dust seal?) from the bottom yoke, you should have 2 cups and 2 cones. Next is to ensure you have seated the 2 new headraces correctly.

Obvious questions first;

Are the cups seated fully in?

Are you sure you got the right bearings for your bike?

Is the bottom bearing fully on the bottom of the yolk stem?

Think Drewpy came up with the aswer to this here

Did it used to have separate ball bearings top and bottom, if so are new new taper ones the correct upgrade for your bike, I only ask this as taper bearings are larger in height than ball bearings, I have just done this to my DTR where the bottom was a taper and the top was balls, and although I used a different larger yolk so got an adaptor made to take up the extra distance and hold the new top taper, I dont think I would of got a taper in the top for the original yolks. pictures could help us out to see whats happened, close ups of bottom, top and bearing races if possible.

PS Tommy posted whilst i was typing

we've seen this before, in the end the chap had to buy new original type ball bearings!