You can do it in MCSkin3D like this:
1. Open your skin in the software and make a backup of it.
2. In the top bar labeling the tools and skin parts, look to the rightmost option: it should say "Steve" or "Alex" depending on which format you're using.
3. Click on it. A menu will drop down, showing various options of Blocks, Entities, Items, Mobs, and Players. Hover your mouse over Players.
4. A list of formats will show up: Alex, Alex (Minimal), Cape, Steve, and Steve (Minimal). Use the minimal option corresponding to your skin format.
5. It will give you a warning screen saying that the conversion process is non-reversible, along with two options on how to convert the skin. Choose Crop.
6. Tada! Your 64x64 skin is now 64x32.

Hope this helped.

You'd need to upload the images to imgur or something, then link those pictures here. When I click on your links it tells me where you have the images on your computer but since only you have access to your C drive that won't help us much. If you have a 64x64 image and you want it to be 64x32 then it must be formatted incorrectly or have much more information than necessary. Since you described your result as 'muddy' I would guess that you tried just re-sizing the image which you now know isn't the way to go. The way I would do it would be to create a new 64x32 image with an alpha background and move each piece I want to keep to the appropriate location in the new, correctly sized, image.

Any further help will require you adding the images in a way we can see/download/alter them.