The embodiments described provide connection structures for dies in an integrated circuit die stack. Each die in the die stack includes a functional circuitry, a programmable array and a programmable array control unit. By triggering the programmable array control unit to program corresponding programmable array in each die of the die stack, signal routes are orchestrated to connect to corresponding functional circuitry in each die of the die stack to enable the entire die stack to meet functional goals. In addition, specific die(s) in the die stack may be bypassed by issuing control command to the programmable array control unit. Die(s) may be bypassed to meet functional goals and to improve yield, and reliability.