[stumped]

well if it comes with options mostly ticked then I guess I ticked them all, way back in the day.
I saw it as a toolkit for fixing stuff, so figured that ticking all the fix it options was the way to go ;that It would skip over un-necessary repairs

tests:
i unticked all the adobe and all the manifest options.
then ran the plug in
most errors go away_ calibre checks stop reporting duplicates and although the book browser pane shows the files sorted in almost alphabetical order , the book chapters sequence is correct when opened in adobe editions

[ almost alphabetical because titlepage.xhtml appears way down the list, yet above anything called section

yet title page is 1st manifest entry so should be ok on KOBO
<manifest>
<item id="titlepage" href="Text/titlepage.xhtml" media-type="application/xhtml+xml"/>

i will go look for the plug in help file and study it.
i should also learn more about the book browser pane in sigl. I get that it is not the sequence controller - that's controlled by the nav file - but confusingly if I move a file up or down in the book browser pane and then safe, the nav fails are updated to reflect that.

main problem with me editingmy own books is that I know just enough to be dangerous - mostly I just fix typos, margins etc and don't go any deeper, but when a book does not navigate the way I want it to ( on a fussy Kobo as a kepub) , I tend to bang it with whatever hammers ( edit / conversion tools) I have to hand, hoping that will do what I lack the knowledge for

in infuriates me whcn kobo shows say chapter 14 in the header even though its showing chapter 15 on the screen. or i tab the previous chapter icon and get the chapter OK but with it being on page 1 of the book according to the slider...That's usually the lack of a cover/titlepage file throws off its count.all that stuff f goes way, usually, once I get the book into a 1 file, 1 chapter, 1 header tag .. format with no exceptions AND with a cover..

modifyepub has been my go-to tool to add/fix a cover, but I can't have it rearranging chapter order. if disabling all it's manifest options is all that;s needed, then great

PS
to actually copy to / test on kobo takes a lot more faffing about so I will do that later.
calibre -> open with adobe editions on PC is my quick check on how well behaved the book is liely to be

and yes. my kobo navigation control gripes would mostly go away if i read it as an epub instead, but I buy kobos in order to use the extra kepub bells n whistles - for better or worse.

so its time to knuckle down & learn more about spines, manifests, OPF and NCX i guess