The top appears to have fairly large internode length while the rootstock appears to have fairly short internode length.
This is almost ubiquitous with commercial JM because they are fast grown to get to sale size as quick as possible. Most of the red leaf cultivars I am familiar with also have long internodes and coarse branching patterns which adds to the problem. I've actually given up trying to develop bonsai from the red JM cvs as the problems outweigh the nice red leaf.
AS growers develop JM bonsai from this sort of commercial start they come to recognize that the basic structure having long internodes and straight sections with little taper is preventing good shape. Eventually most of us have chopped all branches right back to the trunk to start over and grow branching with short internodes and more aesthetic bends.
These trees will be OK for standard starter bonsai but making a really good one is much harder.
I'm a newbie, so take my advice with a grain of salt... I would cut at least one of the (probably the center) branches. There are 3 from the same node and it will create a bulge at that point later. Search bifurcation on here
Again, this depends on the quality a grower decides to pursue. Most people won't even see reverse taper in a beginner type bonsai but if you do aspire to better quality it is best avoided.
When to prune depends on the overall plan of growth. If that section is to be part of the end product it is best pruned sooner rather than later but if the area is higher and will eventually be removed in pruning there's no problem and the extra branch should contribute to trunk thickening.
In this case it is the lowest fork so almost certainly part of the final tree so getting rid of one soon would be ideal. Pruning the centre one is usually a good idea because that usually takes out the thickest so we get better taper from the lower trunk to the new leader. Occasionally that does lead to more swelling as the cut heals.
The centre trunk on this one has really long internodes so it will be hard to get enough branches unless grown as a larger bonsai so removing that part has advantages.
The rear branch also has long internodes but not as long as the centre trunk. That branch MAY be useful as a replacement trunk but check first on the roots to see if the tree can be replanted at an angle to make that new leader more upright.
The best option may be to remove both and just use the front branch which appears to have better characteristics.
Your wires should be anchored in the soil next to the trunk.
Wire only needs to be anchored into the soil if the aim is to bend the lower trunk. Wiring to bend branches can start at any convenient anchor above or below the part that is to be moved.
Most newbie wiring is purely decorative - to make the tree look like a bonsai - so no need for any anchoring at all.
I would remove the center trunk and maybe one of the side ones as well.
