I understand the difficulties with Word when it comes to full-length novels. For short stories, it’s fine, but I spent hours trying to figure out how to easily import chapters from other files–not just the reference link to the folder location, but the actual text. Never managed it. And when you have a several hundred page document, the slow-down is awful!
I don’t know anything about ywriter5–this is the first I’ve heard of it actually–but if the main problem is copy/pasting between programs, it may be that you’re not really indenting your paragraphs in Word, but it’s applying a first line indent to the “Normal” style automatically (or to specific paragraphs). So the tab character isn’t actually there; it just displays as if it is. If this is the case, try this quick fix in Word 2007/2010:
1) Remove all of your tabs. Click “Replace” on the far right of the “Home” tab, or hit CTRL-H to bring up the same window. In the “Find what” field type “^t” (or select the field, click “More >>” at the bottom left, then open the “Special” drop-down and select “Tab Character”). Leave the “Replace with” field blank and hit Replace All. This will delete any tab characters in your document.
2) Put the tabs back into all of the paragraphs. In the “Find what” field, type “^p” (or select “Paragraph Mark” from the “Special” drop-down). In the “Replace with” field type “^p^t”. Click “Replace All.” This will find all of your paragraphs and insert a tab character at the beginning.
If you want to preserve certain tabs and only want to take out the ones at the beginnings of paragraphs (though I’m not sure where else tabs would be…), in the first step find “^p^t” and replace it with “^p” instead.
Hope this helps!