5) Once the liner is nice and clear, why can't you go ahead and SLAM the remaining AA/CA? I'm still unclear as to what the remaining 1-2 week process that I am waiting for is.
Re 5 - when you have metals, you want to entirely avoid Slamming if possible...preferably not just for a week (though the sequestrant instructions only say a week) but if possible, ever. That's because slamming causes oxidization of metals AND consumes/oxidizes the sequestrant as well.
Normally, if using AA specifically, you don't slam to get rid of extra...you keep bringing the FC up until it holds, but to a lower number than slam so that you don't oxidize the metal. Eg. I've added 5 ppm at a time and just continued every few hours til it held.
Regarding your other unexpected results/unintended consequences -- you are using a product with more citric acid in it, not an actual metal sequestrant. We can't predict its behavior because its just not really the same as an AA treatment as practiced/written up at TFP. So it does (apparently) make a difference on behavior/interactions compared to what we normally see happen after an AA treatment.
I'd put my money on the Metal Free as the cause of your other mysteries too

It might be worth contacting Natural Chemistry to see if adding cya while using their product is contraindicated.
If the Metal Free is the instruction telling you to "vacuum out" metal, then the mfg is attempting in essence to leverage the citric acid and its proprietary ingredients to actually cause a combine-and-floc/drop action. This also occurs more overtly with treatments like Alum, which is an actual floc.
Even Metal Magic believes some if the metal will filter out by combining with its HEDP sequestrant and calcium. Jacks believes this also -- I've spoken to their techs at length.
At the end of the day, it seems to me that while some combines and filters out, its a negligible amount and if the metal is in your source water, its pretty much a moot point. But a combo of sequestrant and pre-filtering can ultimately reduce the metal load and reduce the frequency of sequester maintenance doses.
So people aren't technically exactly correct when they say metal can't be filtered out, but in actual real world experience, for our purposes, its never really enough and its not reliable.
I've experimented (in a bucket) with Alum and on my raw well water, filtered out 1.6 ppm of 2 ppm. Then I tried the same test of my pool water (oxidized, then sequestered) and the floc didn't even develop

So there are many mysteries when it comes to metals, and many variables to control.
Said mysteries are exacerbated with various products in the mix. For example, I personally think your cya was sequestered/bonded right out before it was able to actually dissolve via the Metal Free, but I could be all wet on that, so to speak.
Out of all this the most important takeaway for practical purposes is to get some HEDP into the water as soon as possible because HEDP produces reliable results, or I predict your staining will return (as I've seen an cases with Metal Free where it does just that) and avoid slamming if possible.