A "few seconds" should be OK for Apache, unless the time-out value has been set extremely low. I have written scripts which perhaps take 10 seconds or more to conclude without problems (other than users repeatedly hitting the refresh button -- impatient lot they are).

Did you check whether the script really stopped prematurely or whether it was something else that caused it to fail to send all its output to the client? Perhaps if you simultaneously print some debug info to a file (such as a number or timestamp every x lines printed), you can see whether the "break" is in the script (the script did not ran all the way to the end) or somewhere else (the script did ran all the way, but Apache choked on its output halfway through).