[werk_ag]

The problem as I see it is: since my supply is somewhat unstable and at times it constantly shifts in voltage this can confuse the Arduino reference values, particularly when using the 5V (I know this is the reason why Werk_AG has chosen to use the more stable 1,1V internal reference voltage instead for the Solar radiation part).

You are mixing a lot of things.
This 9V (more or less) supply voltage doesn't have any effect on the ADC reference voltages used by the Arduino. This only depends on the quality of it's own 5V regulator, which you can't control (at least keeping the Arduino board untouched).

Returning to the 7809: It have some tolerance in the output voltage, but it does not float... at least in a so large range as you are reporting!

It seems that you are powering it with a problematic power source. Try adding a large electrolytic capacitor (1000uF or more) to input an then check the results.

Ideally, perhaps we could skip linear regulators all together and use something like these DC/DC converters (they can be used in the current boards/design already since they fit the TO-220 footprint) to power the Arduino from a lower voltage and either power the fan independently 24/24h or use some sort of switch to act upon an independent 12v circuit?

If your concern is about efficiency, you can spend the almost 20€ that a TR1- 2490 will cost, and replace the 7809, but it don't gonna give better accuracy on the system, just a little more power efficiency. Anyway, the same result can be obtained, spending less than 1€, with an external DC/DC converter module. Wiring it instead of a 7809 is very easy.



Most of the times, the better is keep the things simple!