1. Did you always/almost always try to two pop whip for the overflow hammers?
2. Did you usually whip right near the finish of barracks/lighthouses to get the max overflow on double hammers?
I'm sure that Bleys answered these better than I could. My understanding of the theory is pretty weak in comparison. I guess I've just got a feel for what works and what doesn't, having played so much civ over the years. Still, I'll have at go a explaining how I do it...
Generally, my whipping cycles are determined by happiness, growth and the tiles available.
I want high value tiles (like the clams or the plains iron) to be worked at all times, so I usually wouldn't whip away the citizens working those, unless I had another city that could take over the tile. For lesser tiles (ie. those without improved resources), I'll quite happily whip the citizens, so long as it still leaves me enough food to regrow nice and quick.
The aim is to work as many (decent) tiles as possible, whilst getting stuff built. The latter is achieved by some combination of working hammer tiles and whipping, with the exact balance depending on what tiles the city has available. For cities with lots of food but few hammer tiles (eg. Akkad), I'll look to run specialists or cottages as it reaches the happy cap. For cities with plenty of hammers (eg. Dur-K), I'll work mines/workshops as it reaches the cap.
Another thing to consider is
immediate need vs.
ongoing efficiency.
If there's a clear advantage to getting something built
now, then it often makes sense to ignore the more efficient whipping cycle. The most obvious examples are when you need a unit at the front line asap, or when you're worried about missing out on a wonder (direct whipping of wonders is highly inefficient, iirc, which is why Bleys and others like to dump whip overflow into them instead).
If, on the other hand, you can afford to wait a little for the build in question, then you can get a higher total output from your city over the course of a whip cycle.
Can you kind of generally describe the mm you were doing? I see where you talk about sharing tiles between Akkad and Dur-K. Can you give an example of how you did this to such a significant advantage (there or any other city)?
This is pretty complicated, situational, and hard to explain (at least for me). But I'll do my best...
In this case, I had three cities (Babylon, Akkad and Dur-K) in an overlap chain, which allowed me to rearrange the tiles across all three to maximise growth, hammers and, to a lesser extent, commerce.
The best example I can think of (and I'm not sure if this ever actually occurred) is as follows:
Dur-K has grown to happy cap using the grassland farms it shares with Akkad, but is waiting for whip

to fade before whipping again. At this time it stops using the farms and switches to the mines (at least as far as food allows - though I may let it starve off some stored food).
Meanwhile, Babylon has been whipped to well below the happy cap, and so needs to regrow as fast as possible. At this time, it is only working two of the clams, as Akkad has the third one.
At the same time, Akkad has reached its happy cap with several turns of whip

still to go, but still needs some food to keep filling up the food bar whilst running a couple of scientists.
So, by switching the farms from Dur-K to Akkad, and the clams from Akkad to Babylon, I can give each city what it needs to be going on with.
Since the food positive land is relatively scarce around here, and since I'm always looking to cut down on worker turns early on, I think this use of overlapping cities has proved quite effective so far. The payoff, of course, is the long term value of Akkad, which will probably end up with none of the overlapping tiles (except perhaps some coasts).
I hope that makes sense...
