Mate,
Sudan and South Sudan were virtually at war a few weeks ago and nothing has really been resolved since. Sudan itself is experiencing 'unrest' in the form of protests and so Sudan is unlikely to want to have you enter across the border area even if you can, nor actually have you in the country at the moment. And it is a border 'area' not a single line to cross with polite immigration on each side.
It is also July - the middle of summer in the Sahara. I was here in April and it was 44 degrees and getting really unbearable.
Looking from a safe distance, I'd go to Nairobi where I now believe you can get a Ethiopia visa again (somebody conform?) and wait for things including the summer period to finish and look forward to Sudan in Oct/Nov or something....
You just crossed DRC I think? Things in the Arab countries are a lot more organised and serious than in the rest of Africa, its much harder to wing it or pay when the military have firm orders etc. The benefits of trying to go via South Sudan don't seem anywhere near worthwhile compared to popping down to Nairobi and getting the Ethiopia visa there. Nairobi is also the easier place to get a Sudan visa, so two birds with one stone....
Just my 2 cents worth anyway....
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