Weirdness after upgrading to v2.3.2

First it’s all probably my fault.But after I decided to do away with my hacked together root index.php and use the WP index.php,instead I’ve noticed some unwelcome changes to the admin and dashboard.
I’ll say it again:I probably did something wrong.But now when I upload an image to put in a post the send to editor button is gone.I also have to use my toolbar firefox extension for web developer to ‘view only this frame’ if I want to be able to copy the image url.
I can’t figure out what is causing my site to act schizo – it can’t find certain things anymore.It’s probably the .htaccess but that was automatically generated when I updated my permalinks.
Bleh…So now the way my install handles images is wonky.
Next is the incoming links that you see on your dashboard when you log in. I saw them once but now I don’t.Where did they go?
The 3rd thing is my plugin for stats.The plugin gives you a widget for the sidebar but you have to type in the url of the stats in the plugin options admin.I don’t want the stats page in my top navigation so I made it a subpage of a page I’m only likely to view.It might be this plus my permalinks structure causing trouble — the stats page is blank.
Another thing is no one seems to be going to my site at all.But that is normal.