I wish the arduino developers program a time out function: pulsein(Pin, HIGH, timeOut); thats would be pretty cool. Any ideas???
There are a number of ways you could implement a PulseIn with timeouts.
PulseIn counts the time it takes for a pin to change to a different state and back again. You would need to add a check to see if a given maximum time is exceeded. The disadvantage of this method is that timing errors are increased by the amount of time to do the additional check. Optimizations can be made to minimise this, such as only supporting 16 bit values rather then the 32 bits used by the standard PulseIn.
A more accurate method is to use a hardware clock to do the timing. There a are a number of ways of doing this but the most accurate would be to use input capture on timer1, either by polling for the register that indicates that a pulse has changed state or by using the capture interrupt.
But you may want stick with existing PulseIn implementation until you are clearer on how the overall system will behave. Your idea of separating out functionality for sensing pulse inputs, driving servos and other functions is a good one. You may find that you can achieve this on a single chip if you want to delve under the covers and take advantage of the timer hardware. Its not trivial, but nor is getting two or three processors reliably talking to each other.
Have fun!