To answer your question about the motherboard. Yes it is fine. The things make that it incompatible are chipset and socket (and intel usually change the socket size with each new generation, so that only even leaves the features of the chipset as a deciding factor). As you have chosen a motherboard with the correct socket for the CPU, then that means it will at least fit, and as the x299 chipset is specifically for the overpriced intel extreme series, then that is compatible with the CPU, so it all works out.

You are confusing yourself with the PCIe lanes. The CPU has 28 direct lanes, the motherboard has slots which use those lanes to provide access between the things that fill those slots (and some other things, like USB ports), and the CPU. Sometimes a board will have slots, that if fully populated required the use of sharing of lanes (thus reducing effective bandwidth to a specific device), or they may use a PCIe bridge. Sometimes you cant even use all the slots if you set certain slots to use specific numbers of lanes.

That all said, based on the hardware items you listed so far, you wont have any issues at all.