1. I think its generally the browser that controls the timeout. You can keep it running by continuing to pass data to it (print some characters occasionally. possibly in a comment) the server can deal with it, but unless its all the server does it's probably not a great idea increasing the timeout. if you do it'll affect all the other pages as well.
2. have the cgi-script act as a bootstrap for the actual script that does the work (exec the program. rather than system; if the cgi script is terminated (the browser is closed) the children would be killed.) (i think)
3. Hmm, havn't read much about mod_perl, probably worth using if you use the script a lot, otherwise , i'm not so sure.

Take a look at Detect Stop Button for preventing timeouts. Its not the primary focus of the node, but its mentioned

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