In a road race if the entire peleton had the objective of trying to achieve maximum speed and work together, average speed and stage time would be a factor, but racing is more about tactics and strategy. To answer the question of improvement over time, one would have to research 40k time trial times through the years, based on similar conditions.
If cycling REALLY gets "clean" I would expect times to get slower rather than faster. I believe that is a challenge in itself, talking from experience going right back to the early 70's. I can't remember many day races back then where we averaged below 42km/h. Nothing compared to below though.
From Wikipedia, I am not sure if this is up to date?
Igor González de Galdeano holds the record for the fastest road stage. 2001 Vuelta stage 9, 179 km @ 55.176 km/h.
Fastest Time Trial longer than 20 km
Greg LeMond 54,545 km/h Versailles - Paris (24,5 km) 1989
David Millar 54,361 km/h Pornic - Nantes (49 km) 2003
Fastest Team Time Trial
Orica-GreenEdge 57.841 km/h Nice - Nice (25 km) 2013
Discovery Channel Team 57,320 km/h Tours - Blois (67,5 km) 2005
Gewiss - Ballan 54,930 km/h Mayenne - Alençon (67 km) 1995
Carrera 54,610 km/h Berlin (40,5 km) 1987