My 318 dyno results

- I can stall the engine if I turn the idle mixture screws all the way in, but it doesn't make any difference on the vacuum at something around 1.5 - 3 turns out.
The only question is whether they provide adjustment. It doesn't matter whether the adjustment range is 1/4 to 1 turn out, or 1.5 to 3 turns out. These needle valves are the last restriction in the circuit. The lack of noticible effect after opening them up more than 1.5 turns could be due the amount of fuel mix available (restrictions upstream and amount diverted through transfer slots), or that a richer mix isn't providing any more power.
- The carb has got a pull off, but it is not adjustable (but yes, I can bend the rods)! When I touch the throttle the choke butterfly closes completely, and when I start the engine it opens up to about 3/8" gap.
If it has an internal pull-off (choke qualifier) the adjustment is under the choke cap as shown in fig. 15. Even if it is physically there, it may not be connected to a vacuum passage. All things worth verifying.

- Another example of the hesitation I get at cold engine. Let's say I finally move up to speed in 2nd gear, barely touching the throttle. it does the 2-3 shift it stumbles, even though I'm keeping the throttle rock steady (barely open).
Yes. A cold engine needs to be richer throughout most of the power band.
- At cruise speed (warm engine) I'm getting 16:1 AFR.
That seems a little high for a radical but if running good, then that's fine.
- Idle vacuum in gear is 13" (and I thought that was pretty good?).
For your cam, seems about right. What's the rpm? 800 or 1200 is big difference.
- I run the Wagner PCV valve in fixed orifice mode.
With 13"Hg at idle, I'd think you could use it in normal load mode, but deal with that later. My recollection is the Wagner allows some adjustment of the air bypass. So the nice thing is you can use this feature to help adjust the throttle blade positions if needed. ( Say for example its idling at 1200 rpm and the timing is already down to 14"Hg or so)

How come I should lower initial timing? From my understanding it should have as much as it can take, without having starter issues when hot? Increased initial timing makes it stronger? I would think less initial timing would make it worse?
The purpose of timing is to develop maximum pressures as the piston is going down - maximizing force on the crank arm around 20 degrees after top provides the most leverage.
Yes we have all observed the engine runs faster with more timing. But its not more powerful. When load is put on it, rpm drops alot.
The starter should not be the determinant of the proper timing at idle. That's OK for racers who have no interest or easy means of adjustment because of what they are doing and the very radical cams etc.
Timing should match the combustion conditions which vary with piston speed, fuel density and load.
For a stronger idle, try something in the range of 14 - 18* BTDC at 650-850 rpm, and AFR mix from 12.5 to 14 AFR. There's no exact number since your engine is different than the next guys this has to be systematically tested 'till you get it as close as you want. But the range of what will work has been pretty well established. You can look at the pre-emissions factory engines to see these numbers are in the ballpark for an engine with somewhat hot cam.