Did you ever figure out a solution to this?
I was thinking of doing something similar. I'd be in Egypt anyway, and would either fly from Cairo to Khartoum, and maybe hang out a few days and look around, or do something more adventurous like take the ferry from Aswan Egypt to Wadi Halfa, Sudan then a train to KRT. But with a US Passport, getting a Sudanese tourist visa... not so easy.
I don't want to chance it, buying a one-way ticket on Egypt Air hoping for a TWOV, then not being allowed to disembark (or even embark in Cairo...) and messing up my whole itinerary.
Any luck finding a tourist visa? Read about a guesthouse Bougainvilla in KRT that can arrange sponsorship letters, but iffy on whether they can get a letter from the Sudan Ministry of Whatever that the embassy in DC needs to issue a tourist visa.
Though with the KRT departure tax of like $250usd in business, plus the $100 for Sudan visa, probably another $150+ in fees to get the visa, $350 flight from Cairo, and the stress/hassle, maybe just better to pay the extra and start in Amman or Cairo. Probably Amman...
Also... how were you going to book this? I've never done an xONEx (only OWEs) -- read that in order to pay the lower fare in a foreign country we'd have to go thru a travel agency there?