A smaller bore certainly helps, but if the cylinders are tiny the heat conduction losses are higher anyways. The difference in fuel consumption between a short stroke engine and long stroke engine of the same displacement is pretty miniscule, maybe 2-3%.
If you're willing to run a diesel (aka heavy polluter), a cheaper mod is to just run a bit lean. Ideally, you would advance ignition timing (any tuning is difficult with Toyota ECUs), but a hack would be to raise the compression ratio just a touch.
For example if you went to 1.1 lambda and raised the compression ratio by 4%, it would probably be approximately optimal (operating near the rev limit probably a bad idea though).
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