Picture a comma after the word "soldier" for a chuckle.

Reminiscent of "Let's eat grandma" vs "Let's eat, grandma".

Or helping your uncle Jack off a horse.

What's correct there, commas before and after Jack?

Depends very much on the uncle's name and occupation, he may well be an equine veterinarian named Steve.

That avoids the worst ambiguity but you still might be helping Uncle Jack murder a horse.

Phrased like that, I suppose that the horse would prefer the uncommaed sentence.

Or you might be helping your uncle Jack by murdering a horse.

With a comma there, it remains ambiguous (is "flies" a noun or a verb?) and even more perplexing.

Think if "flies" is a noun in that formulation you'd put a semi colon or full stop in there and leave it to the reader to ponder if there actually is any connection between the dubious use of the soldier by the student and the ambitious experimentation by the flies...

I think it’s pretty unambiguously a verb in that case. That kind of comma is very commonly used in literary prose and essentially always is an “and” like conjunction that joins multiple actions together.

It would mean "a black soldier and flies."

As in, assuming the grammar on "flies" is wrong and then misinterpreting it?

Otherwise I don't really see anywhere to go down the wrong path except for very small things like realizing a possible noun is an adjective on the very next word.

There's absolutely no grammatical error on the interpretation where the student is out hiring mercenaries to stop the flies' space colonization program.