The Egypt fares you list are comparable to the old Spreadsheet and the amount quoted by Gardyloo above (about $6725 according to today's fx rates). However, when using the online booking tool the base fare prices out at $8519.
Using the EXACT same itinerary with the booking tool, solely replacing the first leg to start in RUH, rather than CAI, I get a base fare price of $6831 (which is comparable to what Gardyloo indicates above).
Both out of CAI and out of RUH I am using RJ into AMM as my first leg. I can't see why the ex-CAI itinerary doesn't price out as the fare listed with Expert Flyer. The price difference from RUH should be minimal, but CAI is probably a much easier place to start (depending on how the political situation evolves).
Itin below if it might help decipher what is going on...
CAI-AMM-CMB-SIN-HND-HKG-BKK-SYD-CNS-SYD-AKL-SCL-GRU-LHR-DXB