A few comments.
The AAV is not electrically powered, it gets heat from the block/coolant that is designed to close the valve as it warms up. You can block off the air connections, the only thing you’ll need to do is feather the gas for a minute or two when you start it cold. That’ll take the AAV out of your troubleshooting, if it is stuck open, you’ll have too much air and difficulty getting the idle down to where it should be.
The vacuum retard, apparently an attempt to improve emission performance. Most leave it disconnected and the port in the intake manifold plugged. Purportedly runs better without it.
The thermo time sensor in the block adjacent to the oil filter is what triggers the cold start injector. You appear to have that missing, hence the switch under the dash. It can suffice but don’t leave it “on” too long, I recall the time is something only about 10-15 secs. The hole in the block where the thermo time sensor resides is a blind hole, no need to seal or block that.
I trust your setting on the trigger points is as per published spec. They don’t require any filing like ignition points, in fact that may damage them. A simple swipe through with some clean brown paper or thin cardboard is all that is needed. A little distributor grease on the rubbing block is helpful.
In terms of setting the valve clearances, stick with the specs, these engines are noisy and that’s just the way it is, and part of the charm.
In terms of your rough idle, go through the fuel injection fault tracing manual step by step to iron out problems.
To set your TPS I found this link most helpful.
https://vcoa.org/forum/9-P1800-1800S...onic-FI-system
Also check and clean the ground wires that attach to the rear of the intake manifold
Good luck and do report back your progress.