If the 328 itself is getting hot, that's usually a sign an output pin has been blowm, and its just a matter of time until the rest of the chip fails.
"there is a tilt sensor attached directly to the 9v pin, the power shouldn't damage the sensor, im just worried that the power going into the arduino through the digital pin from the sensor is damaging the arduino,"
If the 9V was going thru the tilt sensor to an input pin, that could damage it. A voltage divider could be used there to change the voltage swing seen from 0-9v down to 0-5V.
Do you have a link to the tilt sensor? And even better, a schematic of your setup?
And you should download a copy of the Promini schematic, shows the 5V pin (called VCC) that is an output from the Regulator.
This could be 3.3V or 5V, so it is labelled Vcc to be either.http://arduino.cc/en/uploads/Main/Arduino-Pro-Mini-schematic.pdf