You don't need or want 6 counterbored holes in the lower gantry just use the 3 furthest away from the gantry side and the center front one, you can miss the out the center bolt through the gantry side or put it in but with short threads. Reason being the bolts going through gantry side clash with bolts and it's more important you get good fastening into sides so longer bolts needed. Between them, the gantry is going now were trust me.!

Also with the ball screw spacer plates pay careful attention to fastening bolts and that you can actually access them with BK bearing and screw in place because you'll need to adjust these on the machine when setting alignment etc.