Leave the roots alone for now. The tree has than an overwhelming amount of 'power' to quickly throw out some your branches.
Be carefull to remove the young branches that you do not want to develop: When you do this as soon as they show up, you get much less scar tissue on the bark, you could probably just rub them off with your fingers. Also, to encourage nice small branches, I would remove the growing tips every time one or two sets of leaves have formed: That way the internodal distance is reduce a little, and you get a lot of structure (As it will resprout with 2 branches).
You probably want to get rid of the ugly stump that results from blunly clipping away the main stem. I understand that having a leader branch grow out from the top may help. In a few books I have read that Japanese do not like this way of forming a solid trunk. They rather spend time witing, and not have the scars. But if you take the western approach: Grow the trunk. Cut back to 1/3 od desired tree height. Let one leader grow out to form a natural transitution between old stem and leader. Then trim that back to about 1/3*1/3 = 1/9 of the desired tree heigh above the original cut. (The tree becomes 4/9 of desired hieght) and then start building your canopy.
Managed to find the website where I read this:
www.evergreengardenworks.com/trunks.htm