Problem with ledger lines being on top of the stems!! Can I fix it?

Seems like the order in which things are dranw is staff lines, stems, ledger lines, note heads, and what is needed here is staff lines, legder lines, spems, noteheads. I don't think this is something you can do anything about, but is a Job for the programmers to fix the stacking order

Since there are no rules for this, there is no correct or incorrect about it. The order in which we draw things is often important for various reasons that have nothing to do with how it looks when producing experimental scores. I'd say, if you need a different scheme, try exporting to SVG and doing the coloring in a program that specializes in that sort of thing.

See https://github.com/musescore/MuseScore/blob/master/libmscore/element.h#… ff and https://github.com/musescore/MuseScore/blob/master/libmscore/element.cp… ff
for the stacking order, which indeed confirms that ledger lines are after stems, but before noteheads.
No idea what possibly negative effects it might have to re-order them.

Edit: I've tried, changing the order doesn't have the desired effect (no effect at all it seems), strange.

I think the best answer depends on what you do to convert this score to 3D.

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I think Marc's suggestion is on the right track. There are other applications that can manage the display priority after the score has been generated.

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You should be able to File>Export your score to suit that application. From there you can separate your elements into groups, either by moving all elements of a particular color to a "layer"or by grouping all elements of that color and moving the group to the "front" or "back".

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The exact steps and intermediate applications would depend on how you plan to render your score into 3D. I assume you must be planning to do that outside Musescore.