Your right especially the scale of killing in the periphery regions
The scale of the killings and the creation of artificial famines was apocalyptic; savage Arab militiamen beheaded Chiefs, burnt women and children alive and castrated the boys.
The South only took up arms (and lost over 2 million people) because the North thought it would be a swell idea to engage in systematic land-theft of large, mineral-rich Southern territories, like Kafia Kingi.
are there regions that are advocating for Separatism/autonomy in Sudan, Secularisim is being demanded by factions like SPLA are there any regions with significant religious population other than Islam in Sudan
There are currently no secessionist movements in Kordofan, Darfur or Blue Nile; Secession wouldn't be tenable because the Arab tribes that migrated into these Nilo-Saharan and Niger-Kordofan lands in the 14-18th Centuries are so extensively distributed that coherent, contiguous borders wouldn't be possible.
Only autonomy is being demanded by the indigenous populations in the peripheral regions.
The South was the only non-Muslim region; every other region is Muslim.