I think our Hondas' gauges generally over-report speed (not undercount distance).
My 1998 Civic LX speedometer reads about 5% too fast while the odometer is correct. My ScanGaugeII reads the correct speed, so I think that means the VSS is correct. Radar confirms what ScanGaugeII says, and I've analyzed many miles on the turnpike. It really is the Honda speedometer that's off (in my case, anyway).
Perhaps your 14" wheels (instead of the expected 13" wheels) have made up for the error in the speedometer at the expense of the odometer's accuracy? Of course, if your gauges were accurate before the transmission swap, something else is happening.
-Whitey
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