Seems to me that no amount of seeking will let someone find the right file from 90,000. Perhaps you need to offer a different interface to the classical file manager. Let people search by date range or title, for example, or find some regularity in the data which will let you break the collection into chunks. But then you'd probably need a database for that too.

Anyway, perhaps the simplest paging mechanism would be just to pass the name of the file at the end of the previous list, rather than trying to carry numbers? Then you can use something like:

# $filename comes from input
my $marker;
$marker = readdir(DIR) while ($filename cmp $marker);
print "$_: " . readdir(DIR) . "\n" for (1..10) ;
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Which assumes an alphabetical list but should survive deletion of the marker file, at least.

updated to remove stupid mistake before anyone notices.