let me make a stab at beginning the process.(and this is NOT about NII's persoanl anti-semitism)
when one is beginning to try to construct a case against a leader or a system, there are guidelines as to how to do it.
one can begin with evidence that the leader, his underlings or agencies within his direct control broke specific laws on their own books, laws such as murder, rape, theft, corruption, financial crimes, intimidation (if there are such laws available). that means interviewing eyewitnesses to these events.
usually there are episodes throughout a reign that are identified as incidents appropriate for such further study. in the case of NII, i would begin with the pogroms in the pale. as emperor, he had a duty of care for all members of his empire. he was the ultimate guarantor of the law. yet, in the case of the ejws, he failed utterly to keep them safe, from members of his own regime and agencies.
beginning in 1881, more than 30 pogroms were instigated in ukraine, escalating and leading up to the kiev pogrom, the warsaw xmas pogrom, the 1891-92 expulsion of jews from moscow and peaked by the spectacularly murderous events in kishinev in 1903 (+45 dead, hundreds wounded) and odessa in 1905 (+300 dead/thousands injured). in a state with such tight police control as the czarist state, i would examine the okhrana as an agency directly reportable to NII.
there were many testimonies compiled on behalf of a variety of international agencies of the time, so there is firsthand testimony of the particulars. and there was a large memoir literature written by folks who fled. and of course the best evidence: the millions of jews residing in the pale who emigrated rather than live in such an insecure place.
the state sponsored pogroms were more than just riots: they could be called what we today call "state sponsored terrorism" they were part of the policy created by Pobedenostsev; one third to convert, one third to emigrate, one third to disappear.
NII knew that the kishinev progroms were planned; his minsitry of internal affairs was involved, he personally helped to pay for the leaflets to incite the ugly affair.
between oct 11-29, 1905 there were at least 690 pogroms which murdered thousands, wounded thousands more. these pogroms were partially incited by two texts the okhrana (and the court of NII) was instrumental in publishing and disseminating: the protocols of the elders of zion and the great in the small.
since WWII, there is a body of international law dealing with genocide, war crimes, the mismanagement of prisoners of war, making war on civilians. these laws are not retrospective so could not be applied against NII.