Hi Pellicle,
Well done you for plotting a linear tone curve. This is always done when setting up a drum scanner before making a profiile.
I could right a book on the Epson 4990. I have one in the loft which I took about as far as I could go with mods. I owned a 4870 previously.
To get the Epson 4990 to deliver the optimum results you need to do the following:
1) remove the glass & replace with 2mm perspex or similar with a hole cut in the size of the film you are scanning (in my case 120)
2) paint the inside black
3) use betterscanning.com height adjustable holder & anti newton glass or even better a piece of frosted glass cut to size. Set the scan height to about 2.5mm above the glass
4) use Silverfast with 4x oversample & a gamma set to 3.0
5) scan wide open with no adjustments to highlight or shadow
For scanning transparencies, this scanner (or any of the other Epson flatbeds including the V700/V750) has no sharp point of focus. Instead it has a zone, around 1-1.5mm where the image is less soft & just about infocus.
The heat-sink is on the back of the scan head which is just nuts! You will also find the 1st scan after you've turned it on to be the best, with any subsequent scans after it has warmed up in any way being noisier.
There is some more info on scanning here: Dead Link Removed