Like Mark, I use the Minolta 5400, Neat Image, Photokit Sharpener and Photoshop CS, but I use the Minolta software and so far I've just scanned Velvia 50 and some Provia 100f. I have a lot of negative film to scan one day, but I haven't gotten around to my negatives, yet. So, my experience is not identical to Mark's but is fairly similar.
I always scan at 5400 ppi. I understand that if I scan at something like 3100 ppi, what actually happens is my Minolta will actually scan at 5400 ppi and then just resize down to 3100 ppi.
I prefer to scan once, process my photos with Neat Image, PK Sharpener and Photoshop and then resize and sharpen a copy for printing. All my editing is on layers and nondestructive. The entire process is very time consuming. I want to do it only once for each photo, so I prefer to work with and save the highest resolution, best file that I can make with my Minolta.
My files are large, but I manage my work flow so that file size is not a significant problem and storage space is cheap so I'm not concerned about storage.
Also, my experience with Neat Image is different than Mark's. I tried profiling each photo and creating my own Velvia profile with Neat Image using various photos. My results were good. I then created a Neat Image profile using an IT-8 target and my results were nearly perfect. I now get a near total elimination of grain and no loss of fine detail.
Perhaps Mark's experience with Neat Image profiles is due to his scanning at about 3100 ppi. If his scans are actually automatically resized down from 5400 ppi to 3100 ppi, then perhaps the resizing alters the grain structure in slightly different ways for each photo, which prevents him from creating and applying a standard Neat Image profile.
In any event, there is not just one, correct way to scan. My method works for me. I'm sure that Mark's method works for him.