Depends on how you are using your machine. Do the following test:
Open all of the applications you usually use.
Open a terminal window and type top
Find the line that says PhysMem
How much free memory do you have? There comes a point when extra memory will not help performance.
Umm, /usr, /usr/bin and /etc are system directories. The majority of all OSX applications install in /Macintosh HD/Applications. These CAN be moved anywhere you want.
At what point during system startup does the script get executed?? Does it always stop at the same point? Maybe the system is not fully initialised before the script is executed.
Which side is getting warm? Is it near the battery?? As for the short battery life it sounds like the battery is getting a memory. This is where the battery will not charge all the way. Did you calibrate your battery like Apple recommends?? I just got a TI PB today and the manual instructs...
You should be able to access the serial devices by reading/writing to the /dev/XXX entries. I don't know what they are name but the XXX is the name of ther serial port. For example, the modem can usually be accessed via
/dev/modem.