I spent the Christmas / New Year period working in South Sudan, and encountered a surprising number of American citizens there - all of whom were working for various aid agencies. You might want to contact the American embassy in Nairobi, Kenya for better advice, as Kenya is the primary gateway to South Sudan. But, having said that - as recently as 2 weeks ago, one still needed a SPLA travel permit, in addition to a Sudanese visa issued by the Khartoum government. I know they have made peace, but some things take a LONG time to change.
If the US embassy in Nairobi gives you any good news, then try applying for your visa through the Sudanese embassy in Nairobi - they must process hundreds of visas for Americans each month. But - keep in mind that all of those are for professional (aid-related) purposes. There is NO tourism in South Sudan, none, nada, zero.
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