I think your questions are both OK. Your only mistake is that you mention the Present Perfect Progressive (also called the Present Perfect Continuous) but you don't use it.
When inquiring about periods of time regarding activities that still occur/are still true (and are not completed), the right approach in English is always a Present Perfect tense. Whether that be Continuous (+ing) or Simple (+ past participle) (and if the action is completed, but we don't know when), depends on the verb. State verbs (like "be" in your first example) can only be employed using Present Perfect Simple, whilst action verbs (like "study" in your second example) can be employed in PPS/PPC. Using PPC gives your sentence/question that emphasis of "repeated/continuous" activity, but is not mandatory.
So:
How long/How many years have you studied English?
Is just as worthy as:
How long/How many years have you been studying English?
(The same applies to your first example too)
Which brings us to your question of how to phrase your query if you wish to receive an answer using a specific "time reference" (ie "years" in your example). Generally speaking, the native English speaker will likely not worry about the "time" part of the question too much, leaving the listener to respond in the most logical way. In your example, this would likely be in years, or possibly:
Since I was 5.
Of course, sometimes specificity is needed or desired as in your question. If you don't want "since I was 5" type answers, then you need to "lead" the listener, by encouraging them to respond according to the "time" part of the question you use.
How many years? = For x years
How many days? = For x days
Etc.
Consider this last example of a situation where a specific (maybe overly?) response is needed.
A manager has to enter a candidate's information into the following box on their computer during a job interview: Years of higher education studies completed: [ ]
The manager will obviously require a response in years, and so will need to ask his question accordingly:
How many years of higher education studies have you completed?
Note the use of PPS for the "finished action".
Or, if the candidate is still studying:
How many years have you been studying in higher education?
Naturally, my examples work just as well with a more general "time query" (ie "How long?") if the answer doesn't need to be specific.
I hope that answers your question fairly well. Maybe I went into too much detail on PPS/PPC and confused you (I hope not!). As a final observation, I think your first question reads more naturally without "for".
When has is being used as an auxiliary verb, you can simply change subject has to has subject, e.g.
Has she been working at that company for three years?
When it's used to denote possession, you usually add an auxiliary does:
Does his uncle have a big car?
Best Answer
The former is grammatical; it's a direct or normal question.
The latter has not been formed properly. If you omit the question mark, you can form an indirect question in indirect (reported) speech as follows:
To be more polite and formal, you can also form an indirect question in the following way: