Before you prune anything, ask yourself what you are trying to accomplish, and what phase of development are you at.
Are you happy with the trunk like this? That's one possible path. Do you want the trunk to thicken up? That's another.
How are the roots? Is that tree root bound? If so, you might want to do some clean-up on that first. But keep in mind that the amount of root work you do could impact the answers to my previous two questions above. If it's not, then maybe you either play with branches or just let it grow out some more.
When starting with nursery stock, I usually start by making sure the roots are all squared away, and then I use that newly improved root system to get the trunk to do what I want. During that initial process I might do some macro-level pruning, but don't get to fixated on little things that long-term won't matter. During my process of resetting the roots, I'll usually leave most branches in place unless I'm 100% sure that I'll never need them. And even then, sometimes I think twice.
For example, that big lower branch is a great potential sacrifice. Don't cut that off lightly. It likely won't be part of a final design, but it's the best positioned branch to thicken the base of your trunk. You want to let it do it's job before you remove it. Take that approach with everything. Ask yourself, "how can this branch contribute to the trees growth over the next few of seasons?"
Also, in the initial conversion from nursery stock to pre-bonsai, I'll often gradually scale the tree up a bit over a period of years, then occasionally scale it back down again, then potentially do it again. That process of slowly scaling up and down improves the trunk over time.
And FYI - it's not too late to do work on this as long as you do it right now. If you wait a week or two more, you'll just need to leave it alone for a while. I usually do re-pots when buds swell, and will occasionally go just until the leafs start to pop. Anything much beyond that and you're not doing it any favors, and can do some serious damage. The closer to the point it's at here, usually the lighter I go on the root work just on general principle.