To sort things out, I need to know what PCI-e requirements your non-gpu cards have. I hope you know because it will take me a while to work it out.
The PCI-e lanes are divided between the chipset and the CPU.
It has two long x16 slots, one of which will run at x16, or both can run at x8 for SLI or 2x Crossfire.
The motherboard also has three x1 PCI-e slots.
There are also two older PCI slots.
All of these share the 20 lanes available.
There are also six SATA ports a SATA Express port, and an M.2 Port. You cannot use all of these at the same time. If the M.2 is being used, then either the SATA Express, or two of the SATA ports are disabled. When M.2 is used, it will give you 10 Gb/s, using two 6Gb/s lanes to do it.
If all of those cards are working on your existing motherboard, then they will work on your new motherboard. I'm guessing that they each use only x1 PCI-e lane, for a total of 5, but they will cut your GPU down to x8. x8 + 5 * x1 = 13 lanes The SATA, SATA Express, and M,2 share a different four lanes used by the chipset itself.
None of this really has anything to do with M.2 itself, but rather how has the board manufacturer assigned the limited lanes to the various devices that need them.
The Z97 Guard Pro is a little different.
It has a x16 and x4 long slot, so cannot do SLI, which requires 2 x8, but will do Crossfire which only requires x4. It also has 4 x1 slots, and no PCI slots at all. It has no SATA Express, and to get that, and it's 10 Gb/S you need to use an adaptor in the M.2 slot.
I hope that this clarifies things.