Use several factors to choose which option will be better.
Start with roots: Find the best view of the nebari regardless of trunk or branches.
Next check trunk line. Look for the best trunk flow, bends, taper, lack of scars, etc.
Follow that with branches but as this tree doesn't have any skip that.
Look for features - dead sections, shari, etc.
Finally look for faults - crossing branches, dead sections, hollows, reverse taper, etc.
Now consider whether any of the choices above coincide. Usually the choice with the most positives will be the best option to choose.
If you plan to remove that lowest trunk I'd try to steer clear of that as the front as it will leave a big scar for many years. That side also has the big root sticking out so not so good there either.
2nd pic gives the least visible scars but also least trunk taper and not much bend either.
3rd pic shows best taper though still not much but nebari is one sided there.
New buds will usually form closer to the chops so chopping too high can be counterproductive and you'll need to try again in a couple of years if no low buds pop.
Agree that JM can be fickle. I've also had some failures when chopping bigger trees to bare wood but most will grow.
Shorter is always good for bonsai. Need to allow for growing an entire new apex which will typically be as tall as the lower trunk so initial chop at 2 feet tall will often yield a completed bonsai at around 4 feet????? That's a real big bonsai!
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