There's plenty of roots, you're not hurting anything by going down to find the nebari.
Nurserymen are notorious for planting too deep in the pot.
Keep digging.
Cut the top layer of roots off with sharp scissors, flat across the top.
You can also shear off half the foliage, so you can see what branches you have.
Remove almost all the flower buds. (Keep maybe a dozen so you can see some pretty flowers next spring.) But since you're growing this for bonsai, you need to get the tree to spend it's energy growing new branches, not expending it on flowering. Removing the flower buds will really accelerate the growth next spring.
Really, on something like this, you're really not going to be able to use 95% of what's there. What you're looking for is a trunk line. Pretty much everything else will get pruned off. It will bud out new branches. And you can train those horizonally.
When looking for the trunk line, choose the front based upon the nebari. (So dig it out!) Then look how you can create the best taper.
When you prune, don't leave stubs, nor leave deep gouges in the trunk. Carefully carve it smooth, then use cut paste immediately.
Good find!