I'll address your points in separate posts, as they are involved. First there is an initial point as to who and what Judaism comprised pre AD70, which is a grey area in the "New Perspective" material I have read to date. Prior to the 20th century, many Jews concurred with Louis Finkelstein's words that Pharisaism before AD70 was "practically synonymous with Judaism" on a religious level. There were also the Essenes and the Sadducees. But as to the great mass of people, Josephus in Antiquities speaks about the Pharisees' great public influence and power. In recent years Josephus has been attacked by sceptics e.g. Morton Smith "Studies in the Cult of Yahweh," 1995, Ch.9 "Palestinian Judaism in the 1st century." He posits that Antiquities' reflects an emphasis on Pharisaic predominance post AD70: he asks whether our post-70 sources have not all read this later situation back into their accounts of pre-70 Judaism. However, this scepticism may be untenable, given the bible supports Josephus, and there is no overriding reason to suppose that what was the case post AD70 is not a reflection of pre-AD70.
You might want to consider reading that book on the Pharisees that I recommended. There were swings of power prior to the time of Jesus, with the Pharisees falling in and out of power, depending on the time period. Anything after the fall of the Temple (post-70s AD) would not provide an accurate reflection of what Jesus actually said or meant. That is one reason why I place the writing of Matthew prior to that event. Rabbinic Judaism evolved after 70 AD and Pharisees may have been influential in that development. During Jesus' time, the Pharisees numbers were in the single-digit thousands. They were lay teachers, who had limited authority in terms of the Temple. Generally, they had other work and Paul is a good example.
One thing I would encourage you to do is study what is called common Judaism of the time. There are overlaps between the sects and the common people (the
ʽAm haʼaretz, or "people of the land") technically did not fall into any of the major groups.
As for Josephus, he views Pharisees as follows:
3. (12) Now, for the Pharisees, they live meanly, and despise delicacies in diet; and they follow the conduct of reason; and what that prescribes to them as good for them, they do; and they think they ought earnestly to strive to observe reason’s dictates for practice. They also pay a respect to such as are in years; nor are they so bold as to contradict them in anything which they have introduced; (13) and, when they determine that all things are done by fate, they do not take away the freedom from men of acting as they think fit; since their notion is, that it hath pleased God to make a temperament, whereby what he wills is done, but so that the will of men can act virtuously or viciously. (14) They also believe that souls have an immortal vigor in them, and that under the earth there will be rewards or punishments, according as they have lived virtuously or viciously in this life; and the latter are to be detained in an everlasting prison, but that the former shall have power to revive and live again; (15) on account of which doctrines, they are able greatly to persuade the body of the people; and whatsoever they do about divine worship, prayers, and sacrifices, they perform them according to their direction; insomuch that the cities gave great attestations to them on account of their entire virtuous conduct, both in the actions of their lives and their discourses also (Ant. 18.3) (Flavius Josephus and William Whiston, The Works of Josephus: Complete and Unabridged (Peabody: Hendrickson, 1987), 477.) Note that numbering for Antiquities varies depending on the translation used.
In his evaluation of the Sadducees, he notes that they are influential among the masses. (There is some dispute as to whether Josephus was a Pharisee. He seems to have received instruction from multiple groups, and as a priest, held them in some destain. However there are places where he seems to agree with them.) They also were known to be lenient in judgment, which is reflected in Gamaliel's assessment of the Christians in Acts 5:33f and the judgment of the Pharisees in Acts 23:6-10. They were also present in the church (Acts 15), which tells us that Pharisaism, in and of itself, was not incompatible with Christian belief. John provides us with two Pharisees who also are friendly with Jesus.
How does this compare to Jesus's assessment of them in Matthew 23? Given the other evidence, does it not seem more reasonable to suggest that Jesus' condemnation of the "scribes and Pharisees" is dealing with a subset, perhaps a particular group of Pharisees who are also scribes or even priestly Pharisees? The Temple authority seems to be the dominant antagonist for Jesus.
"Josephus tells us, first, that on account of the Pharisees' domination of religious and social norms, even the Sadducees defer to their authority (Ant. 18.17). Second, although Josephus himself was a rather outspoken critic of the Pharisees' behavior, as we have seen, he too claims that he "followed" their way when he began public life (Life 12b).65 It seems plausible, then, that any first-century Jew, such as Jesus, could concede the Pharisees' legitimate social-religious role without taking out membership in the group and, indeed, while pointedly criticizing their conduct .... Notwithstanding legitimate scholarly suspicion about the motives sources on the Pharisees, the evidence of Josephus seems to require this group did exercise the dominant religious influence in pre-70 Palestinian Judaism."
"Pharisaic Dominance before 70 CE and the Gospels' Hypocrisy Charge (Matt 23:2-3)", Steve Mason, The Harvard Theological Review, Vol. 83, No. 4 (Oct., 1990), pp. 363-381
Steve Mason is a fine Josephus scholar and I have discussed certain ideas with him in the past, particularly on the audience of Romans (where we disagree). But note what he says above - "Notwithstanding
legitimate scholarly suspicion about the motives sources on the Pharisees, the evidence of Josephus seems to require this group did exercise the dominant religious influence in pre-70 Palestinian Judaism." Scholars do disagree here. They definitely were influential, but they did not dominate the Temple or the Temple authority. Herodians dominated the political landscape. The Essenes saw all as corrupt.
Mason has a chapter on Josephus' view of the Pharisees in the book I mentioned and summarizes his conclusions at the end. You might want to get that book to see what his conclusions are. The book is more recent than the article you reference.
As to the specific immorality and sins of the Pharisees, one article is "The Pharisees and Their Legal Traditions According to the Dead Sea Scrolls," Lawrence H. Schiffman, Dead Sea Discoveries, Vol. 8, No. 3 (2001), pp. 262-277. From the critiques of the Pharisees by the Essenes, and from "later rabbinic reports" their sins linked to immorality were those of advocating the marrying of one's niece, polygamy and remarriage after divorce, which the Essenes associated with fornication.
That is one I have not read, so I will limit my comments. As I noted above, Essenes saw all (except their own community) as corrupt. I agree that Rabbinic literature does not speak kindly of the Pharisees. However, the Essenes faded from view after the Temple fell, so I would not conflate their view with later Rabbinic views of the Pharisees.