1. "Indicate whether you intend" is most correct among those options, but The Meal is right. Rephrasing is better. "Do you intend to follow the regulations?" followed by a 'yes' box and a 'no' box should be sufficient.
2. "Whether or not" means "whether"; the "or not" is redundant.
3. "If" sets up the antecedent (the protasis) of a conditional statement. For this reason, the imperative sentence "Indicate if you intend to follow the regulations" is grammatically analogous to the imperative sentence "Dance if you're happy". (In casual usage, people tend to use "if" in place of "whether"; the latter will probably die out along with proper sequence of tenses and other nuances of counterfactual and modal expression.)
"Indicate if you intend to follow the regulations" can be rearranged to make its logic more clear: "If you intend to follow the regulations, then indicate."
Of course, "indicate" expects a direct object, and the thing being indicated is the fact that "you intend to follow the regulations". So the rearrangement can be expanded to "If you intend to follow the regulations, then indicate that you intend to follow the regulations."
That leaves open what should be done if you do not intend to follow the regulations. Presumably, indicating that would be helpful, too. So a better instruction would be "If you intend to follow the regulations, then indicate that you intend to follow the regulations, and if you do not intend to follow the regulations, then indicate that you do not intend to follow the regulations." Indicate if you do, and indicate if you don't. Indicate X or indicate the contrary of X. If only the language afforded a way to capture both sides!
That's where "whether" comes in. Reveal whether the victor is China. Do it if China is the victor and do it if China is not the victor. Explain whether this grammatical form is proper. If it is proper, then explain; and if it is not proper, then explain.
Thank you, grammar Jedi, for your help. For the document, I did advise rephrasing the sentence as a question per Meal's suggestion, and suggested as an alternative the "whether" option in case that would be too radical. I also enjoyed reading Grundbegriff's analysis. DBT's suggestion might not be appropriate on the form but we'll try it over the phone.
I'm also glad a couple of you are open to sharing snacks with Heather Lagenkamp.