This is basically a question of parsing: which element goes with which. "Signal plan" is a heading, and "call signs, frequencies, code words, pyrotechnics, challenges, and passwords" are the types of signals that have to be planned.

You quote an example in which "plan-signal" appears hyphenated, but that hyphen is being used as a dash, equivalent to a colon. Here's an example of the same thing with a colon, which clarifies the meaning:

"Signal plan: call signs, frequencies, code words, pyrotechnics, and challenge & password"
https://www.atu.edu/rotc/docs/2_LDAC10_Maneuver_Handbook_26_...

The "signal plan" is the list of agreed signals planned before the operation, so that everyone knows what they are. "Call signs" is the first element in the list of types of signals. Call signs are unique identifiers for transmitters, so when you get a signal you know for sure where it comes from.
https://en.wikipedia.org/wiki/Call_sign

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Note added at 41 mins (2017-09-14 06:55:18 GMT)
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Sorry, I meant an example in which "plan-call" appears hyphenated.

It could have been expressed like that, with "of", but "of" is not necessary if there is a colon or other punctuation after "Signal plan", as there is in the example I've quoted. A dash (—) could be used instead of the colon, and it sometimes is, as in this example:

"Signal plan — call signs, frequencies, code words, pyrotechnics, and challenges and passwords."
http://library.enlistment.us/field-manuals/series-2/FM7_7/CH... (on p. 5)

The point is that "Signal plan" is a heading. It's common practice, in lists of this kind, to put a heading, which is a general category, followed by details of what is included in that category, with punctuation after the heading: colon, dash, even just a full stop.

The list that begins with "call signs, frequencies" gives the details of what is included in the signal plan.

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Note added at 13 hrs (2017-09-14 19:52:18 GMT)
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A colleague has pointed out to me that the correct reading of your text is probably different from the one I've given you here.

The implication of what I've been saying, which I should have stated more clearly, is that there is an error in your text: that some punctuation has been omitted by mistake after "Signal plan". There are other examples of your text on the Internet. I found just over 20. Nearly all of them have some punctuation after "Signal plan". Usually it is a dash or hyphen (used with the same function as a dash):
Signal plan — call signs, frequencies [...]
Signal plan-call signs, frequencies [...]
Sometimes it is a colon:
Signal plan: call signs, frequencies [...]
And sometimes the list after "signal plan" is in parentheses:
Signal plan (call signs, frequencies [...])

In all these cases, "Signal plan" is a heading and what follows it indicates what is included in the signal plan.

However, apart from your own text, there are a couple of other cases in which there is nothing between "Signal plan" and "call signs", etc. The colleague who wrote to me pointed out that we don't have to assume that this is a mistake; it makes sense if we take "Signal plan" as a noun modifier: a noun phrase used as an adjective that modifies what follows.

So there is a signal plan that covers call signs, frequencies, code words, pyrotechnics, challenges, and passwords, and "signal plan call signs, frequencies, code words, pyrotechnics, challenges, and passwords" means the call signs, frequencies, code words, pyrotechnics, challenges, and passwords included in the signal plan.

Another document in which "signal plan" is used like this as a noun modifier is this one:

"(k) Determine logistics support.
(l) Identify signal plan call signs, frequencies, code words, pyrotechnics, challenges, and passwords."
https://rdl.train.army.mil/catalog-ws/view/100.ATSC/03696C98...

This means "Identify the call signs, frequencies, code words, pyrotechnics, challenges, and passwords included in the signal plan".

I hope this makes it clear.