Sure I can handle this for you, what is the format of the serial stream to the processing application.
You can sent out a continuous stream and use the timers and some pin ints to do your counting of pulses on etc.
The serial stream would just pick up the current values and squirt them down the line for you.. If you keep the format brief then you can get a lot of data down the serial port at high speed.
Take a quick loot at my website WWW.EmbeddedAT.com
and see the kind of projects I normally get involved in.
Then if you want to chat about your project more then drop me an email to Peter@EmbeddedAT.com
or here on the forum