These two references seem pretty self-explanatory. It is not really important to understand the more technical info, it is just included in case you start asking questions like, "Yeah, but how good were these dudes in the test?"
J Sports Sci 2001 Dec;19(12):969-76
Comparison of physiological responses to morning and evening submaximal running.
Martin L, Doggart AL, Whyte GP.
School of Sport, Performing Arts and Leisure, University of Wolverhampton, Walsall, UK.
in6078@wlv.ac.uk
The aim of this study was to assess the effect of time of day on physiological responses to running at the speed at the lactate threshold. After determination of the lactate threshold, using a standard incremental protocol, nine male runners (age 26.3 +/- 5.7 years, height 1.77 +/- 0.07 m, mass 73.1 +/- 6.5 kg, lactate threshold speed 13.6 +/- 1.6 km x h(-1); mean +/- s) completed a standardized 30 min run at lactate threshold speed, twice within 24 h (07:00-09:00 h and 18:00-21:00 h). Core body temperature, heart rate, minute ventilation, oxygen uptake, carbon dioxide expired, respiratory exchange ratio and capillary blood lactate were measured at rest, after a warm-up and at 10, 20 and 30 min during the run. In addition, the rating of perceived exertion was reported every 10 min during the run. Significant diurnal variation was observed only for body temperature (36.9 +/- 0.9 degrees C vs 37.3 +/- 0.3 degrees C) and respiratory exchange ratio at rest (0.86 +/- 0.01 vs 0.89 +/- 0.07) (P < 0.05). Diurnal variation persisted for body temperature throughout the warm-up (37.1 +/- 0.2 degrees C vs 37.5 +/- 0.3 degrees C) and during exercise (36.2 +/- 0.6 degrees C vs 38.6 +/- 0.4 degrees C), but only during the warm-up for the respiratory exchange ratio (0.85 +/- 0.05 vs 0.87 +/- 0.02) (P < 0.05). The rating of perceived exertion was significantly elevated during the morning trial (12.7 +/- 0.9 vs 11.9 +/- 1.2) (P < 0.05). These findings suggest that, despite the diurnal variation in body temperature, other physiological responses to running at lactate threshold speed are largely unaffected. However, a longer warm-up may be required in morning trials because of a slower increase in body temperature, which could have an impact on ventilation responses and ratings of perceived exertion.
Int J Sports Med 1997 Oct;18(7):538-42
Circadian rhythms have no effect on cycling performance.
Dalton B, McNaughton L, Davoren B.
Centre for Human Movement Studies, University of Tasmania, Launceston, Australia.
The aim of this research was to determine if circadian rhythms have an effect on time trial cycling performance of 15 min duration. Seven males (Mean+/-SD): age, 22.3+/-4.9 yr; height 179.0+/-7.9 cm, body mass 74.5+/-15.5 kg; VO2max 68.0+/-5.7 ml x kg(-1) x min(-1) who were all competitive cyclists or triathletes with previous experience in laboratory testing procedures volunteered to participate in this study. Each of the seven subjects underwent a series of four tests; one VO2 max test, and three 15 min maximal performance tests, at varying times during a 24 hr period. Testing times were at 08.00-10.00; 14.00-16.00 and 20.00-22.00 hours. Heart rate was recorded during the last 10-15 seconds of each minute and blood lactate levels were taken at 5 and 10 min during exercise and again immediately post-exercise. O2 consumption was measured continuously using open circuit spirometry. RPE was measured using the Borg scale at 5 and 10 min during, and again immediately following the completion of testing. Resting oral temperature was the only variable to show a significant time of day effect (p<0.05). Oral temperature during the afternoon was higher than both morning and evening results by 0.76 degrees C and 0.09 degrees C respectively. Total work (kJ) and average power output (W) were recorded at their highest during the morning session and reached a trough during the afternoon session, but these differences were not significant (p = 0.9997 and 0.9972 respectively). The results obtained in this study indicate that while certain biological rhythms are present, they appear to have no effect on this type of cycling performance. Although athletic performance may be enhanced by training programs that are compatible with an individuals body clock, the ability to perform and train at various times has an adaptive response which appears to over-ride these naturally inherent rhythms.
Bottom line: It certainly FEELS harder to run fast in the morning, but physiologically, it isn't. Try a longer warm-up to raise your core temperature, and stick with it a while as there seems a need ("adaptive response") to simply "get used to it".
Certainly many top athletes will pay attention to doing some of their training at race time in their preparation build up. Doesn't make sense to be only used to running hard 6pm if your race has a 9am start time.