|Problems? Is your data what you think it is?|
Why don't you use the sliding window technique already discussed?
If you don't destroy/recreate the variables but just change the content, your memory consumption will╣ be minimal.
substr manipulates the content of strings.
pos returns the position of your last regex match.
So only one global variable $window of fixed size holding two current blocks could do and whenever the pos of a match leaves the first block you have to shift a new block into $window.
╣) well, as long as Perl doesn't do very (unlikely) weird speed optimizations.
This code is an almost perfect example of what I meant: Matching in huge files
The differences are the temporary variable $block which could be optimized away and the handling of pos. Instead of adjusting the window at "halftime", pos is adjusted to the window. Actually I think this is even smarter than what I planed...