We know of no organised birding tours to Southern Sudan.
We know of no birding guides in Southern Sudan.
Several airlines fly to Juba and there are international flights from Khartoum, Addis Ababa and Cairo. There are buses daily between Juba and Kampala, Uganda. Most of the roads are little more than dirt tracks made impassable after heavy rains. Travel is likely to be difficult and requires preparation in terms of permits and security checks. Care should be taken with the use of binoculars (permit not necessary) and cameras (for which a permit is required) near Government and sensitive sites such as bridges and airports.
Visas are required for most people entering South Sudan. In theory, visas are available on arrival at Juba airport for $100. However the rules surrounding their issue are unclear. Immigration officials will often invent rules to suit their own needs. At the very least, you should have an invitation letter from a local company / organisation and you will need someone with local connections to be sure of getting a visa. It is better to obtain one in London, Nairobi or Addis Ababa before arrival.
Travel in some of the border areas with Sudan is still risky even though there has been a cease-fire in the long-running civil war and a peace agreement is being discussed. The best advice is to check with your embassy before travelling to or around Sudan.
Other safety and health issues are no different from those in many African countries. Guidebooks, travel companies and websites provide much of the advice one needs, but key points warrant repetition here: (1) be aware of the risk of malaria and seek current advice, sleep in a sealed tent or under a net and take prophylaxis as recommended; (2) always ensure you have sufficient water and some method of purification (even if this comprises a pot and a campfire for boiling); (3) do not underestimate the danger of being in the sun for too long, ensure you use sun-block, drink plenty of water and wear a hat; (4) be aware of the risk of AIDS; (5) ensure that you take a reasonably-equipped first-aid pack with you including supplies of hypodermic and suturing needles.