I have written about the Ustasha, their ideology and the relation to Bosnian Muslims here and here.

To answer your question with some of the info from these answers: The Ustasha Muslim connection was not really an alliance since especially the Bosnian Muslims did not have something along the lines of centralized political authority. The Ustasha used the Bosnians as pawns in their anti-Serbian policy and the Serbian Chetniks also committed violence against the Bosnians because certain Chetnik bands (again, a problem of centralized authority) had a program of ethnic cleansing and that drove Muslims in the arms of the Ustasha. On the other hand, other Chetniks regarded the Bosnians as Serbs of Muslim faith.

As described above, the Bosnian Muslims were caught between various fronts and different factions and communities reacted in a variety of ways from seeking out the Ustasha to joining the Partisans to wanting the Germans to take over. In that sense, these alliances did not reflect a long standing alliance rather than a reaction to local conditions or in case of the Ustasha a political or racial ploy.

Also, I would be very wary to draw a direct line to the 90s since a lot of stuff happened between 45 and 90 especially when it came to national policy within Yugoslavia (such as Bosnian becoming its own republic and nationality in the 60s etc.).