I read somewhere that some vehicle manufacturers add extra moly to the original factory fill. As for draining out any shavings left in the engine from the factory, the oil filter will remove anything large enough to be harmful that gets through the inlet strainer.
Also, I found that the bike will start to roll backward a little easier if it's in neutral or the clutch is pulled in. The first couple of times I did it I had the bike a few inches from the garage wall to ease my concerns about it falling over to the right.
With a long enough cable lock you can run it through the sleeves of your jacket as well as the helmet and secure them both to the bike when it's too warm to wear the jacket indoors.
I used the string method from Motorcyclist magazine.
Learn Simple Motorcycle Wheel Alignment - Motorcyclist Online
It worked perfectly after I had the same problem after changing tires on my Z750s. Just remember to re-center the strings on the rear tire after each adjustment before...
One thing that I found very helpful that's not usually mentioned, is to pull the clutch in or put the bike in neutral since the bike has to roll rearward slightly as it's rising on the center stand. Also, for me, I pull mostly up but slightly rearward with my right hand on the frame by my leg as...
If you had to turn the screw twice before it made a difference, it sounds like the TB's weren't reliably resting against the idle stop thus causing an erratic idle.
I used the 2X4 under the car frame rail to break down my tires, but sprung for Marc Payne's wheel balancer with my car jack stands. The results were perfect.
Get an infra-red temperature gun and check the temperature of the exhaust headers. That should tell you which cylinder is mis-firing. Since the last thing you did was to change the plugs, I'd then check the connections for the plug. If it's still not idling smoothly with all cylinders firing...
What happens if you wait a few extra seconds after you turn the key to "On" before hitting the "Start" button? The PC III might need a few extra seconds to boot up before it can do it's job.
It sounds like one carb isn't staying full enough. Use an infra red temp gun on the exhaust headers to see which cylinder it is, then check the needle valve and float to make sure there is sufficient movement to allow enough gas into the carb.