I just re-read your original post, and was reminded of this:
there are about 500 times less 1's then 0's
So for the average item, only 30 features are true, which changes things. You still can't do an all-to-all pairwise comparison in any reasonable amount of time, but you may be able to e.g. recursively partition your data by the feature closest to a 50/50 distribution, then find closest matches once you cut the comparison set down to something reasonable. If something simple like that won't work, you should look into dimensionality reduction, e.g. via random projection or PCA.
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