Looking over this again,
you are using 7/8 pex (why in the world your supplier keeps suggesting that is beyond me, but it is there now)

You have 3 zones
Zone 1 is stapled between joists under floor with three circuits (600')
Zone 2 is in a newly poured concrete slab (300')
Zone 3 is upstairs, stapled between joists (200')

The Takagi runs as described;
Also, I called Takagi and the discovered that the required temp diff varies according to GPM for example, with outlet temp set at 131F:

at 3 GPM return temp needs to be 121F for takagi to fire (10 dT if I'm understanding correctly)
at 2 GPM 116F (15 dT)
at 1 GPM 101F (20 dT)

Looking at the pump curve on the X block http://media.blueridgecompany.com/documents/X-Pump-Block.pdf (keep in mind both pumps on x block are delta T and variable and the unit is using outdoor reset built in) and the fact you have 7/8 pex (ugh) your head is low,
You could loose the zone pumps you have, replace with 3 zone valves and drive the whole system off x block system pump,
I doubt you would need a buffer tank, I suspect the X block would modulate up or down and relate well with the delta T on the Takagi.
But also keep in mind, to use the x, or better said when isolating the system you will need a water make up and temp/pressure gauge and heat side expansion tank.
Dan