I guess my concern was: should I try now just to get the tree full of growth close to the trunk? I was worried that if new growth hardened off it would be impossible to bend or shape later.( I guess I could always get back budding to try and form new branches)
Dunno where you live (amend your profile????), slowgrow, but Bougainvillea are tougher than many people think. If you don't go much below 28 degrees in he winter, you might want to put it in a sunny, protected (wind) spot in the ground for a year or two because, frankly, I don't see a bonsai in there yet.
When you do start to prune (and don't remove that lower branch -- shorten it) these things root so well and easily from cuttings that is the better way to go. It's some times awkward to air layer a small branch like that.