You must crop all borders when relying upon VirtualDub's histogram. I see that while Sanlyn's guide mentions this, he doesn't specify that it's an absolute requirement. And I recommend you overcrop while measuring, since there is little downside to doing so. Too bad it's too late for him to edit the post now. I think he did say that you should crop when teaching you directly in another thread.

The reason is that the "black" borders are actually superblack. They're horizontal blanking and they're at blanking level, which in the case of our video system means they're 7.5 IRE darker than video black. They should be at digital 0. So if you leave them in the image while using VirtualDub's histogram, they should be red. Bringing them out of the red area means you're washing out your entire picture.

For PAL and NTSC-J, this theoretically doesn't matter since there is no pedestal and blanking = video black = 0 IRE = digital 16. I would still crop them while adjusting regardless, otherwise you're still calibrating to the non-video area and assuming that whoever made the video set black in exactly the perfect, technically-correct spot.

Essentially, yes. On a totally black screen, Loose Minimum "should" be 16-17.* On the waveform display, you would see a line hovering along the bottom brownish edge. Then the same thing for whites, but in reverse: Loose Max ~235. But I personally prefer to rely more on Maximum ~235 and let Loose Max hover lower, since clipped brights bother me much more than crushed blacks.

* For retail tapes & LDs, you will find that some black screens have different levels than others. You want the one that actually matches your program content. So don't really solely on a black screen at the start of a disc. Check dark scenes in the video too.

It can be, but your whole goal was to optimize the proc amp setup. Stretching it afterwards will tend to introduce more banding. And like with audio, the SNR would be lower.