FWIW, I recently had a very quick turnaround in Port Sudan. Not so quick in Khartoum on the leg back...
I'd look into something like this:
Great Circle Mapper
LDZD - Very cheap, quick turn, friendly.
LCPH - PM me, I can assist you there. Route via RDS to avoid Turkish overflight costs.
HSPN - quick and painless, relatively civilised. HELX or HEMA as alternates. No crew visas for a Sudan turnaround/tech stop. Fuel was waiting for us before we landed.
This way you will avoid Egypt and save time...
Then on down!