I'm still not convinced that you're not making the problem harder than it should be. A select that has to compare all entries for one key vs all entries of every other key, even if the db is indexed by that key, is fairly intensive. It doesn't surprise me that it required some tuning to get the time down. Simply populating a hash, though, with the values you get and undef as placeholders, should be quite efficient.

That said, you might check Chart::Plot to see if it will do what you want. It does not require uniform length data sets, per the doc.