Instead of doing your for loops like this:
for ($i=0; $i<count($input); $i++) {

Do them like this:
$count = count($input);
for ($i = 0; $i < $count; ++$i) {

This way the count function isn't called for every loop. Thus speeding up your script

Also ++$i is slightly faster that $i++

I will work on that in the next version..