Ben, how come you didn't "retire" your car and start a fresh one after you did the swap? I think if it's sufficiently different to use different EPA ratings, then it's different enough to start fresh - so your lifetime average isn't artificially low.
I talked to matt about this months ago and we decided it would be unfair to reset my lifetime like that. I mean, I did after burn that gas in that car, for me it's more about cumulative use that bling bling. Besides, it'll always be my first car no matter what happens with it, <3
I would lean to the EPA values for the VIN of the car. Any modifications that you have made are just that modification it does not however change the registered name of the car. Just my 2 cents.
stock numbers are the best way to gauge what you've done to the car...i'm saying this and i just swapped an si tranny onto my hf engine...haha...i'll be in the negative, maybe...i'd like some of those civic hybrid wheels