While trying to understand the design of the crank of your bike I came across this website. You may find it interesting:
Honda Cb350b4 (general Export Type Km/mile) parts list partsmanual partsfiche
When you are analysing the problem of your crank, pay attention to the line of the crank as shown on the picture below:

I might be wrong but from the drawing below I understand that when pressing the crank at locations circled in red if it is not done properly, the centre line of the crank will be wrong and will lead to the problem you are facing. I can't see any dowels to ensure that the crank line is correct when assembling. As mentioned earlier, put a dial gauge to the crank to find out where the problem is happening.

If all else fails come down to Pindi for a day on any Sunday and I'll introduce you to my Lathe guy and help you get it sorted out. My guy is very experienced and has all the measuring tools.
Regards