Be very wary of differing fuel origins and spec variations. Search for information on Speedbird 38 .. very probably caught out by fuel waxing .. and there have been more than a few other incidents.
Having been involved on the tech side of an investigation into a similar event, I have read a range of relevant technical reports on the subject which suggest that the problem is one which warrants cautious consideration by pilots operating some susceptible aircraft (due to unfortunate fuel system design matters) or aircraft generally on long range operation in cold air masses. Quite a while ago now so I would have to dig deep to find the report on the particular event.
Your suggestion that fuel flow (or, perhaps, fuel quantity indication, depending on fuel tank arrangements) irregularities might be the first indication is consistent with what I have read elsewhere in the literature.
For the pilot's problem, it is not so much a matter of the fuel mass freezing as precipitating wax bodies which then tend to gum up the works, as it were. As the fuel temperature continues to decrease, the proportion of waxing grows ..