Hey David
Ok, I didn't realize it was built from an example, so I've got it now.
You are almost there, I'm able to get it working however there are a few issues that I was able to identify and may have contributed to it not functioning as expected.
1) Initialize your shift registers and feedback nodes.
2) Your PID isn't tuned properly try setting Inflow Rate = 1000 L/sec, Off Limit = 20 cm, High Level Limit (setpoint) = 10cm PID Limit = 5 I was able to get PID control of the tank, but its oscillating quite badly so experiment with the settings till you get it right.
Some suggestions to make your code better.
1) You have subvi's with uninitialized shift registers, have an initialize Boolean that initializes the shift registers with appropriate default values.
2) Your subvi's are a little confusing as you are not following the connector pane convention of inputs on the left outputs on the right, if you are running out of terminals to follow the convention then try a connector pane pattern with more terminals or try using a cluster, ie your PID inputs could be input as a cluster.
Hope this helps