i don't know how to make games, so take this with a grain of salt.
what if you had a refresh button. when clicked the system takes a moment and numbers all the wires, inputs, and outputs. After doing so it sets a 3rd value that says this node is connected to these nodes, and here is the wire data as well. Then after its mapped your board, it the recalculates the new nodes and the sizes of the chips.
then when its done refreshing, it displays the changes.