Night Mode Back to top position

That's because of this CSS:

body.wp-night-mode-on .main-navigation .main-nav ul li:hover>a, 
.main-navigation .main-nav ul li:focus>a, 
.main-navigation .main-nav ul li.sfHover>a {
    background-color: #181b1c;
    color: #888;
    transition: none;
}

It looks like you're missing body.wp-night-mode-on in front of the two other selectors.

For the article, .separate-containers and .wp-night-mode-on are on the same element, so the selector should be:

.separate-containers.wp-night-mode-on with no space.

Menu on worked
but article one is not

CSS :

body .separate-containers.wp-night-mode-on .separate-containers .inside-article, .separate-containers .comments-area, .separate-containers .page-header, .one-container .container, .separate-containers .paging-navigation, .inside-page-header{
	background-color: #151515;
}

and also give me sidebar widgets css too and comment area too

Got it somehow with

.seperate-containers.wp-night-mode .inside-article {
   background-color: #212121;
}

in some cases the css is direct .wp-night-mode-on rather than body.wp-night-mode-on. is there any explaination for this ?

That part doesn't matter. The first one had a second .separate-containers defined.

So we good right please can you have look at web so i can put it in live production

Applied on homepage
Applied on Post Page, Sidebar, Comment area
Applied on Error Page
Applied on Archive Page
is there any page i am missing ?

Looks good to me :)