None of these are asking for an instrument, Jim. You could ask what the difference is between instrumentum, auxilium, and res, but hopefully you don’t need to do that. Certainly a common question is Quo modo? (How?, By what means?).
“Quo instrumento” literally means “by what tool”, so that actually is a good way to ask “by what means” or “with what instrument”.
“Quare” means “how” but can also mean “why” or “for what purpose”.
“Qua” can also mean “how” generically, but it also means “by what route”, as in “how did you walk here.”
“Quomodo” is more generic in meaning. The answer to that may be an adverb, but it could also elicit an answer using an ablative of means. So it might be asking about instrument or manner or something else.
Another option is to ask “cuiusmodi instrumento?”, meaning “by what kind of tool” or “by a tool of what kind”?