$pid = open3 ($zipin, $zipout, $ziperr, system("cmd /c zip.exe -FF \"$
+mainfilepath\" --out \"$ziprepairedwordfilepath\""));
[download]

Thats broken. system read that. And read IPC::Open3. Your calling open3 wrong.

$zipin = print "y\r\n";
[download]

Thats broken. print read that. Perhaps another monk can comment if the wait() is correct.