Plugged in shield off by one, now all analogues read high
There is not (yet) enough information to be certain, but it seems likely that you have damaged the Arduino.

If damage has occurred it's more likely to have been caused by what happened on the other side of the board, where pins carry power supply voltages. You do not say what your power source is or where it is connected (USB, 5V in, Vin, ...) but I'd guesstimate that the connection of UNO 5V to Shield 3V3 allowed back feed into the UNO by any of a number of possible paths. UNO Vin connects to shield ground and a second UNO ground connects to a second UNO ground - so if the UNO was powered via Vin you'd expect the power supply to have been shorted. This might damage some power supplies but usually not. 

Can you please advise what voltage was connected and to what pin. And do shield pins all offset by 1 on the other side, as I've shown?