In general the auxiliary verb you will use depends on your precise sense of time frame and mood in the sentence. Since you do not say what it is, it is difficult to know which is right for you. And, there are some usage problems in the second sentence beside the missing auxiliary verb.
Here are some suggestions:
According to the World Bank, approximately two-thirds of the data that have been used to calculate business indicators are based on a specific reading of the law.
1) "World Bank" requires an article 'the' (this is just because of the way they style their own name)
2) "two-thirds" is correct. In general, think of "ratio" words as literally being a number of denominator shares grammatically: "one-fifth", but "three-eighths".
3) "embedded in doing" is incorrect use. "embedded in" is used to indicate that one object was contained in another object. The "container" object must immediately follow "in". "Business indicators" are "calculated", and the data is "used to calculate it": in some part of the process of calculation it is utilized.
4) The main idea of the sentence is that the business indicators can come out one way or another, depending on which reading of law you use; they are not universal. To signal this, we should say that they are calculated using a "specific" reading of the law. Now a reader will now that a different reading of the law might give a different value of the business indicator.
5) have been here indicates that the situation described in the sentence happend during some time in the past, continued through the present, and is possibly or likely ongoing. had been or was would indicate that the situation is possibly or likely no longer occurring. might have been or could have been or may have been if we suspect but are not sure that the situation occurred.
Also note that "data" is a strange word in that it is the same plural and singular, in most speech. That wasn't always true, so if you are writing for someone else, or have a style guide, you need to check if it recommends using the singular or plural form or the older use of datum for the singular.
Ironically, however, investment has been lackluster in the period that India’s ease of doing business ranking has improved.
This one is easier. The tense needs to agree since the time frame does not change. Continue using present perfect with has. The addition of that is not required, but makes the sentence flow better. If the improvement continues to the present time and is ongoing, you could also use the present perfect progressive tense:
Ironically, however, investment has been lackluster in the period that India’s ease of doing business ranking has been improving.