JD, I think I'm a bit late, but your approach won't work. I'm running both Nikon scanners with absolutely perfect results. However, if you want to 'batch' a strip with 3 6x6 images and need to crop, you'll be in trouble: VS applies the crop to the batch, not just to a single image.
But here is the trick: Batch preview your images. Go to the first image, apply your crop (color tab should/could be unchanged), change the batch to i.e. frame 1, proceed with image 2, apply your crop, change the batch to frame 2, and so on.
Ultimate solution: Batch preview all images, select a crop that fits them all, batch scan them, crop them in any application. Make sure you configure your settings to 48bit @ highest resolution, filter -> infrared clean to LIGHT and hit go.
You can set a frame/crop that matches all images and then save this as a template. The frame/crop can be moved left/right top/bottom for each single image - this is a per image option. You can even rotate the crop for one frame without influencing the others as long as you don't modify the aspect ratio of your frame/crop (I mean the marquee or rubber band).
You can use different 'images' for the display of your histogram:
check this link (I'll add more information over the next months here).
Right on top of the article I've posted a scanned slide which shows the power of VueScan.