This is what we're going to be doing: re-painting a scan to make it neater, higher quality and pretty (yay!). Basically, we're turning this into this!

Right, the first thing I did with my scan was do a basic filter-cleaning. (See Shinta's tutorial for that part.) After cleaning, I started working on the flowers.
Using my tablet (but it also works with a mouse), I picked a round, hard brush, size 9, and lowered the opacity and flow to around 63% and 74% respectively. Eyedrop the color you need. Making a new layer above the original scan, I start dotting the "highlights" of the flowers:

The same thing goes for the rest of the flowers. I made layers below the white petals and did the shadowed petals and the in-betweens:

After working the flowers, I did the girl's kimono. I also "vectored" the black parts of her kimono to make it look neater.
Next, I started working on the tree and ground. Again, make a new layer and eyedrop the color you need:

The only difference in this step compared to the rest is that we're going to be smudging. So, I chose a hard, round brush, size 8 and put the strenght between 50-60% and started brushing in an up-down direction on the highlights and shadows:

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