I have come to realize the pour time is not as important as watching the color phases of the shot. Of course seeing and stopping at the right color is timed to a degree.
What I would like to know, and my question to the learned is; when do you begin the clock--the moment you throw the lever or when the flow begins and is visible?

I've seen people say its the moment you throw the lever, mine is exactly 25 seconds untill it starts to blonde from then, just over 20 from when it starts to pour.

From the moment you start the pump. From the FAQ, see Timing of espresso extraction starts when? and a follow-up discussion. That said, it's only a guideline and even the SCAA barista competition technical judges accept anything between 20 and 30 seconds. Personally I haven't used a timer in ages.

Covered in the FAQs (also easy to search for fwiw):

FAQs and Favorites

Specifically:
Timing of extraction starts when?
Timing a double shot

...you say it does. Just be consistent.

If the time starts on the first drop, it translates from site to site. If the time starts on the pump, there is a considerable variation in time until the first drop.

From the time the pump is activated.

Why?

The timer is timing the extraction time.

Extraction begins at initial water contact, which begins when the pump is activated. Thinking it through yields the common sense reply: start it with the pump.

I have further confused myself by having a 5 seconds delay relay on the pump, so I get 3 bar preinfusion. I have wondered if that 5 seconds really counts as 2, because... OK, I am overthinking it now.

That three seconds counts as 3 seconds into the time.

Water is in contact, thus, it counts.

Jasonian wrote:From the time the pump is activated.

Why?

The timer is timing the extraction time.

Extraction begins at initial water contact, which begins when the pump is activated. Thinking it through yields the common sense reply: start it with the pump.

While technically correct that some 'extraction' of the coffee begins on water contact, it's nothing we consume until it exits the portafilter. Extraction begins when the coffee flows. Before that, it's simply moistening the coffee.

Riddle me this : Image two H-Br's with the same machine, grinder and coffee. JoVibe trundles over to PaulPlumb. Does pulling a 30ml, 20 second shot from pump start give the same cup? Not even close. The vibe has a about a 13 second 'flow' vs 17 for the plumb in, a ~30% discrepancy. Much closer results are obtained when time starts on the first drop. Obviously, longer, ristretto pulls should differ less.

As long as we are consistent and state when we start time, we have a usable baseline.