Agree the Nile Road is a big pain. In 2011 we picked up a tourist police escort which meant stopping and waiting every 20 mins or so whilst they handed us over to the next lot of police. Very busy road - mostly though towns, not very enjoyable.
What sort of tyre problem? You can drive the desert loop entirely on excellent tar if you want. You can still see the deserts from the main road. In fact in the White Desert the main tracks (helpfully colour coded) were very easy going - compacted sand - and some of the loops are just off the road. It is an incredible place to camp and the oases towns are so laid back I'd go that way even with car trouble. One of the highlights of a three year trip for us.
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