Where are they and are the ones in jyotyu used?

It uses the same graphics as the normal coin but with another palette.
So the graphics for them are in the jyotyu animation file: d_2d_A_J_TEN_jyotyu_ncg.bin

You should also edit the normal jyotyu file too. Because when you enter the level the "unanimated" coin is shown for a very short period.

Where is d_2d_A_J_TEN_jyotyu_ncg.bin?
Can the editor open it?
And how can I make red coins look like normal coins?

1. In the BG_NCG folder
2. Yes. Just doubleclick it, and then doubleclick the palette and click "Add all"
3. Change the colors in the palette from red to yellow.

Thanks
on a related note:

Could you recommend a simple editor (like Micro$oft Paint) that supports transparency for Windows (or cross-platform)?

Try paint .net or GIMP.

I would recommend Paint .net, since I find it easier thatn GIMP and it supports transparency too.
_________________________

What I meant by "like paint" was not as fiddly as GIMP or Paint.NET for now I will try Game Maker sprite editor.