I believe you're using Windows10, correct?

Before you do this, make a copy of the skin in its current state "just in case".  I would hope you already have a backup of it in its original state.  This change will fix #3 and will have some affect on #2 and #4 (it's all related), so make the change and look at it and go from there.  Also, if you do this for Windows10, you will lose the transparent Explorer backgrounds should you for some reason decide to use the skin on Windows7, so be prepared for that.

The problem is semi-transparent explorer window backgrounds.  Delete these 2 sections of the skin within SkinStudio:

Backgrounds /Edit Explorer Backgrounds / Active window (Glass) and Inactive window (Glass)

Delete those 2 sections by clicking on the "help" tab within the each section and clicking on the text in the lower right corner "Delete this skin section from the skin".

I'm sure the selection color can be changed, but I'm not quite sure exactly how.  Sometimes it's an image, but that looks like a System Color to me.  I don't have that particular skin.  If you want to poke around, go into "Change skin colours" and click on the dropdown menu next to "Show me the skin colour presets" and select "Show me the defined system colours".  Look for that particular color, I'd guess it might be "Selected Item" or "Menu Highlight".  If you change anything make a note of what it is before you change it to test (it's amazing how quickly I can forget 3 numbers).  (Do me a favor if you find it and let me know what it is - I don't have it in my notes  ).

Or you can of course wait for someone who knows exactly what it is 

Well you're on the right track.  You would need to do the same thing for the Per Pixel frames, and that's what Explorer will use.  You'll need to find the Per Pixel frames in Tron and copy them over to Samurii.

When you're doing this type of thing, you also need to take note of the painting margins for the pieces in the old skin and change them to that in the new skin so that they look right.

Also, in my case, when I'm doing heavier tweaking like this I prefer to create a new substyle in the skin I'm changing.  That way I can have my hacked-up version alongside the original version and use either one on a whim. 

[Which System Color did you end up changing above? - The color picker is covering up the name, e.g. "Selected item"]

Thanks a lot, once more, for all your help, DaveRI. I got it to work, but seeing as the standard preset of the TRON borders was blue, and my whole theme was built around black & red, the blue really didn't fit in so I decided not to use them after all. Unless... there isn't a way to change those PerPixel Glyphs to another color, is there?

Well, even if there isn't a way, thanks a lot in any case!

Thanks, I'll take a look at it.

Another one:

See the "Hard Disk Drives (4)" I encircled in blue? Is there any way I could change that black font to another color, like say white? I tried looking in "Change Skin Fonts, but there are so many fonts in there, not all applicable, and I'm really not sure to which font in SKS this applies.

And now I've loaded up several dark skins with Explorer on "This PC" and I'm getting the feeling that text may be locked on black.  I'd love to know how to change it if it can be.

Yup, Dave is correct. It is a good idea never to make a skin that you cannot read the text on. If you lighten the explorer background some, it would help.

Quoting DaveRI,

reply 14

Thanks guys.  Now that I've seen it I'm sure it would've nagged at me 

No problem always here to help when I can along with Lightstar. If Kevin comes back maybe he would want to make the background a bit lighter and you can advise him on doing that. Unless he can live with the Black text. 

Dave you know a lot about SKS maybe you should be making skins.

First of all, glad to finally meet you in the forum, Neone6, you're an inspiration to me!

Secondly, thanks to DaveBax, I completely forgot about OldNewExplorer, forgot I installed it. I unchecked that checkbox, reloaded my explorer and voilà:

Admittedly, the sides aren't from TRON, they're from the skin Legend, made by - again - Neone6.

I also have to admit that I did my very best using Photoshop to replace the blue color of the Legend skin (I mean the side borders) with red, but that didn't work out equally well everywhere.

A new question has arisen, though: see how the top (caption) bar isn't really aligned with the left (& right) side border image? Is there any way I can correct that?

Thanks for the quick response, Neone6. I tried that before, I opened up the top caption image in Photoshop (CS6) and used Image -> Image Size to make it a few pixels smaller (9 pixels in total, later on I tried with 50 pixels smaller) having unchecked the "constrain Proportions" checkbox, I saved it as another targa image, imported that one in SKS but it made absolutely no difference.

Think it'll make a difference if I widen the side images instead?

Yup, you were right. It's weird that you have no choice but to change the size of the sides of the window in order to make it fit with the top & bottom. Changing the bottom or top doesn't change a thing, it would appear. Nevertheless, I got it to work to the best of my abilities. Ain't perfect (especially at the bottom) but for now it'll do:

 (EDIT: imgur doesn't do my screenshot justice, it doesn't take into account the transparency near the right & left edges of the screen)

New question though (and to think I started out with just one question ) : see the refresh icon near the top of the screen, and see the search icon to the very top right of the screen? Well, you can't see it, but there's text there somewhere. Something along the lines of "Search this PC". Is there any way to make that text white or something? 

I tried looking in here already: SKS -> Edit Explorer/IE Shell Parts -> Edit Explorer Parts -> Search Field Background -> Extra Settings (really, Stardock knows NOTHING when it comes to usability, if you ask me ) and there: "Search text colour" which I changed to white... which resulted in no change.

You guys got any ideas?

Kevin, next time draw a circle or something on the area you are talking about. I believe you are talking about the text on the right side between the refresh symbol and the search symbol. Guess i'm saying what you said. That text is in the search area, it is the same text that will show on the search area on the Startmenu. That text is also hard coded by the OS and can't be changed.

The only way to see it is to make the search area image a bit lighter. That image is in the Edit Explorer Parts. NOTE: It will also chang the color all the way to the left just right of the arrow after "this PC