silversol,
I am the member that holycow was referring to. I have a few ideas.
1. If your 99 civic has a TCM (a computer that controls the shift solenoids and torque converter lockup), I think you could work out a way to manually override it (with buttons on the steering wheel) so that you could force it to upshift at low rpms and immediately lock up the torque converter. You couldn't get rid of the added drag of the transmission's ATF pump, but you should get closer to to efficiency of a manual transmission in city driving.
2. Maybe you could swap a final drive set with a better ratio into the transmission (assuming you could find a set that would fit)
3. Try a warm air intake and a hotter thermostat
4. If you have a big budget, there is a company that makes the Drivematic automatic clutch:
http://www.youtube.com/watch?v=ApQ_f0btB50
I called them a few years ago and they charged about $9K to install it- they would not sell the parts outright. This could enable you to get another VX.