scrambler

What version of weaver are you using, and is it basic or pro version?
If you want the menu centered there is an option in Main Options > Menus > Menus Bar Layout Section for that.

If you just want to shift it right a bit, you can add the CSS below in Advanced options > Head section > Custom CSS Rule box
#access {padding-left:50px;}

Also you have chosen to used a fixed width non responsive mode. This is a bad Idea in this day an age where many mobile device need the site to be responsive.

Finally, in the future, you should use the main support site as you will get a lot more attention there 🙂
http://forum.weavertheme.com/

be specific on WordPress and weaver II version (should be 2.1.10)

If you are using WordPress Custom Menus in Appearance > menus and you are saying that when you go back in there items are gone, this is a WordPress issue.

I remember someone mentioning a problem when you have a LOT of menu items and having to change some WP settings in that case.
http://forum.weavertheme.com/discussion/6924/menu-broken-with-wp-3-6weaver-please-help#Item_10

If you don’t have a particularly large number of menus / items, you may want to try and redo the WP 3.9 update from Dashboard > Updates

I am not sure what you mean by uninstall / reinstall, but in order I would try

Delete all weaver Theme folders using CPanel file management, that would revert wordpress to a default theme like 2013, then see if you can install weaver II from scratch.

If not I would get my Host provider to restore the last backup before the wordpress update.
EDIT:cross posted with esmi, this is the same principle as what he mentionned, just more radical (delete instead of rename), So you should try the rename first 🙂

Are you speaking of the grey border that shows up when you hover over the image, or one that is there all the time ?

Because on IE, your images have no grey border in their normal state, I only see one on hover.

I also see your rule
.ngg-gallery-thumbnail img {border: 2px solid #FFFFFF !important;}

It is active and doing its job. It is overriding the initial nextgen rule
.ngg-gallery-thumbnail img {border:1px solid #A9A9A9;….}

and if I remove your rule, the thin grey border comes back. If this is the border you are trying to hide, and it is not hidden when you look at it, you may have a cache issue, check on another computer and another browser.

You can also use your browser developer tools, click on one of the images and look at all the rules being applied to see if you see both the original grey border rule and your white one.
If you do see both check which one is overriding witch.
If you don’t see both then you likely have a local cache issue, because I do.

The repeating pattern could be done with a Background image custom CSS rule for the sidebar, but extending the sidebar to be the same as the Content area regardless of its size is a complex problem.

The pro version does have an option (flow color to the bottom) that uses a JavaScript to calculate the content area dynamically and resize the sidebar accordingly, but this not a simple CSS fix.

If you come to the weaver forum with a link to the pages that have sidebars, we can have a second look to see if there are any workaround specific to your configuration.

make sure to post a link to the pages in question.
http://forum.weavertheme.com/

In the future, just use the weaver forum, you will get faster attention 🙂
http://forum.weavertheme.com/

In Weaver Admin > Mobile tab > Disable mobile support.

But this is not a great Idea and will make you site hard to use an navigate on mobile. May be you need to elaborate why you want to do that as there may be some ways to fix the issue bugging you 🙂