I've been using one of these: SparkFun XBee Explorer Regulated - WRL-11373 - SparkFun Electronics to interface an XBee with my Mega. If I want to read the RSSI output, will I need to take the RSSI through a level shifter up to 5v in order for the mega to recognize the HI state of the pulse? Or is 3v sufficient?
The Arduino reads an input on most pins as HIGH when the voltage hits at least 60% of VCC. So if your Arduino is running at 5V, anything higher than 3.0V "should" read as HIGH.
Unless you are playing with different crystals, PWM won't frequency/period change. I mean, you can manually change it... but that requires code. The PWM hardware and the UART hardware are isolated and one does not affect the other.