I've built this machine 100 different times in my head!!!

[Iwant1]

I've made a quick drawing of how I will be connecting them. A screw goes right through the bottom extrusions and screws up into a T-nut slotted in the top extrusion. The screw head will be sunk into the D slot for my profile rails to sit flat on the extrusion. Hope it clears it up a bit.