Hello,
I use the LS5000 with the automatic slide feeder. I have had good results, and agree about using only one type, or similar types, of slide mounts at a time.
One gotcha that took me a while to figure out is that a slide will often "catch" as it is on its way into the scanner. It turns out it is catching on the next slide in the "in" tray. The solution is to simply pull the "in" stack of slides back just a bit to free the current slide to continue into the scanner. You have only a few seconds to do this before the scan is canceled, and you will have to restart scanner and software. Sometimes I will go through 100 slides with no catch, and other times it will be every other slide.
Also, I have found that none of my attempts at profiling the scanner yield results as good as Nikon's internal color management. This is somewhat frustrating because I would like to do the conversion out of the scanner's space, rather than letting Nikon do it, but the reality seems to be that they do a better job. It seems that they have built-in calibrating routines (every few slides), and conversions that work hand-in-glove with the hardware.
I typically scan to Adobe 1998 (though the scanner can be fooled to convert to ProPhoto), use Digital ICE for dust and scratch (either normal or fine), have auto focus and auto exposure ON, and pretty much nothing else, doing all other adjustments in PS.
Other than the occasional slide feed issues I have had a good experience. For the purposes you describe I would scan in 16-bit TIFF, at 2x or 4x sampling. At 4000 dpi, these will take 3 or so minutes each
I do find flare to be an issue when there is a very low density area next to a high density area. Though dust on the mirror is supposed to be a contributor to this, I have noticed it from the outset. Perhaps it is worse now? I haven't made the comparison. Neither have I had the mirror cleaned. . . At the times when flare is an issue, I have simply addressed it in PS.
Best Regards,
Michael Morrison