Rudi - Wadi Halfa ferry is fine - it goes every Monday afternoon. See my reply to Pete Sinclair's topic "Egypt - Sudan border", last item posted on 11 April - getting a motorbike on probably won't be any difficulty, but you can check with the people mentioned.
Regarding South Sudan, the war is still going on, despite periodic alleged ceasefires. Everybody goes through Ethiopia to reach Kenya and you would be best advised to do the same. Riding through on a motorbike, you might be lucky and make it, but:
1. You might get shot by anybody who took a fancy - south Sudan has been a warzone for decades and is not like the friendly relaxed north - there are lots of armed people around. If Juba is still under siege, you will also have to cross the frontline - which would be rather difficult.
2. You'll never get permits to travel this route, so you'll have to somehow dodge the police until you get far enough south to be out of govt controlled areas. Then when you reach Juba - which is again govt controlled -the police will want to know why you travelled there without a permit, and could decide to do anything they like with you.
3. It is highly unlikely you will find any fuel along the way - the whole economy has stopped in the south, there are literally no vehicles in the rural areas and so one imagines no petrol stations.
Unless you hear that any of this has changed - which it hasn't for years - I suggest you go through Ethiopia.