I suspect you might have over-voltage on 5V - this would explain the destruction of one device and general unreliability. You say the onboard 5V regulator isn't working, so powering from Vin is not a great idea. But if the Arduino is working at all then there must be some voltage on the 5V...
The decoupling capacitor on the sensors might be reducing spikes/noise and helping stabilize the supply but if the regulator is blown it needs replacing before using Vin.