Get a good clearing agent in Egypt
Whether you intend to drive through only or import the bikes in Egypt, you'll need a good (meaning honest) clearing agent at destination. I trust many shipping companies will provide you quotations and only part of the total indicated amount will include the costs for working with a clearing agent at destination. The trick is to pick the right clearing agent in Cairo. Ask for details and investigate first.
My humble experience with importing stuff in Egypt (4 times so far) makes me recommend not to go for the cheapest option necessarily as in most cases the estimates you'll receive will unlikely cover for clearing costs. Only respectable and well established international firms will do it in a transparent and effective way, respecting all legal obligations and putting your papers in order so you have all in hand when you want to leave.. Others will build fees as they go, and trust me it can get quite surprising. Last time when importing 5000 USD worth of accessories for my Land Rover revealed quite complicated and I was completely kept in the dark, not to mention the language issue, and I could never get a clear answer, not even a receipt of any kind. I ended up paying a hefty 1000 USD custom charges, and for why? it remains a mystery... One can get mad.
When I imported my KTM in 2008, the shipment arrived in Alexandria, and I had to get a Cairo Traffic Authority guy to travel to the Mediterranean port to inspect the bike from there to clear customs. Sine I had installed the luggage rack prior to departure, he decided the bike had been modified (nothing less) and then had to undertake an additional inspection in Cairo prior to registration. All in all it took 3 days of painful work and costed about 1500 USD to import and put a license plate on the bike. Just carry plenty of small notes throughout the process. If you just pass through Egypt, you won't normally have to pay the 1200 USD I paid in duty to get a regular / permanent license plate. But if you just pass through, you'll need a carnet and the deposit for Egypt is 8 times the value of the bike. One could simply wish sending the bike to the next destination and pick it up there to avoid dealing with the Egyptian bureaucracy and arbitrary taxation system.
Riding in Egypt is extremely dangerous but a lot of fun when you get out of Cairo and off pavement. I find importing the bike was a good thing in the end, I still enjoy it and hope to explore more of the desert side before it gets too hot. For me it was worth the trouble and the cost. Just dealing with the right clearing agent who will help you through the whole process is definitely a must. There are plenty of them. Good luck!