From experience driving it, I would say the main factor is the lean burn system. However, that takes into account that I trained myself in maximizing the use of lean burn in normal driving conditions.
There's a Honda white paper out there somewhere that spells out the increases in %s and attributes them to various technological advances, but as you said, it's mainly VTEC and lean burn, which are all part of a very large system. VTEC-E by itself I imagine will do very little without leanburn, though it should be better than nothing.
Finding an HF transmission will probably help worlds more. You should be able to dig one up for free.
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