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Hi. I've read the reply on standing up to take the measurement but am still a bit confused. Should I be getting into a position where the score comes out highest (which for me is sitting) or should I be standing to give lower reading? I have been sitting which gives a higher score and lower HR. Also I have found that if I do it first thing before getting up it is not my best score - I don't drink caffeine but do get up have a drink of water and move around a little (maybe bit of stretching) and use the loo. After that seems to give highest score on HRV. My readings for this week are

HRV HR
90.5 42
90.1 45.4
90.2 44.1
87.7 44.5
91.6 47.5
87.1 43.9

The first one below 90 was after doing short fast run the day before. The last one (today's) is after a 4 hour run yesterday. I was hoping for a red but came out amber.

Hi Darren

Your high HRV scores and low resting HR indicate that you're a fit guy, so I would definitely recommend you to do the test standing up if you can.
Remember it's not the absolute score that's important for detecting the impact of fatigue and recovery, it's the changes from one day to the next and the average trend line (the solid blue line on the chart).

Similarly, the exact time of the test is not important - what matters is that it's a convenient moment in your morning routine when you feel relaxed and that you can repeat every day and stick to. The time you suggest sounds perfect for those reasons.
Regarding the amber traffic light you had today - looks like you recovered pretty well after the short fast run, back to an HRV over 90. Therefore the score you got today after the 4hr run of 87.1 indicates a first day of significant fatigue, which will give you an amber - ie you should not do a very long or intense training session, but you don't have to take a complete rest day. If your score is low tomorrow, then you will get a red, indicating that the fatigue has started to become cumulative, and that your body needs more time to recover.
On this last point, I'm just finishing a free booklet on training with HRV that will be downloadable from this site, and that will give tips on both interpreting your results and speeding up recovery.