I have 3 road bikes and they have different wheels, Easton low profile light-weight clinchers (EA90SLX), Reynolds 32mm carbon clinchers, and 50mm carbon tubulars. I don't think any of those wheels make me ride faster or slower over a whole ride.

I got a TT frame a couple of years ago and started to work on riding with a lowered front end. Since then, I've slowly moved the stem on my road bikes lower and lower. On my main bike, I've got no spacers under the stem and I've just started using a -17deg stem. Doing this has made a big difference in the speed of my rides. Looking at average speeds over similar routes over the last few years, I'm definitely going faster.