Music Case

While pages ain't a application you can just download individually as it's apart of the suite (or you can't to my knowledge)... If you download the full installation of your version of IPS then unzip it, then go into the applications folder you should find the 'pages' folder.
Just copy the 'pages' folder into your applications directory via FTP then go into admin and it should be installable again.

I sussed it out, i'll be making a tutorial soons

I can only think of one thing that maybe the problem, which is if you're using a custom theme then it might not be up to date with IPS4 meaning it will look like there's no styling,
...
A solution would be to log into ACP, find support and click "something is'nt working correctly" and run all the way through it so it disables your apps and restores the default theme, that should fix the issue however then your apps will be either outdated or completely incompatible in which case you need to enable them one at a time to see if they work and if they don't then keep them disabled until you find an IPS4 alternative or an updated version for IPS4.
You would have to repeat this for the theme too, keeping it disabled until you remake your IPB3 theme IPS4 compatible or until you find an IPS4 theme.
I don't know how you upgraded but you're meant to disable all applications etc and i don't know if this is necessary but i usually revert to default theme until iv'e finished the upgrade.
Also because your ACP is also messed up, navigation maybe hard so if you can't find support then CTRL+F and search for support it should find it nice and easily for you.
If you'd like I can help out if you don't mind me logging in but that's completely up to you PM me if you'd like.

You could go about this multiple ways both include creating your own BBCode:
Method One:
making your own bbcode, allowing the {option} feature and just putting {option} in the required field like this, however this will leave you vulnerable to all sorts of malicious code as anyone could insert any code and put it in.

Method Two:
Making your own bbcode to be <iframe src="http://store.steampowered.com/widget/{option}/" frameborder="0" width="646" height="190"></iframe> where people can insert the ID of the steam store page and it will embed the steam store widget like that.

Nav bar menu items can be added // removed by going to:
ACP
>>System
>>Menu Manager

or do you mean visually (colors etc) edit your menu ?
As for your other issues, not sure about either but if you wanna link to your board i can have a look...

This ? 
https://invisionpower.com/files/file/7796-automatic-post-when-moving-topic/
Download is here if it's the right thing, a quick look, looks like it is:
 

or add this to your custom.css..
#elUserNav .ipsUserPhoto img { border-radius: 100%; } Tested on my board just now, also looks a lot nicer than the square thanks for the idea..
Edit
Add this to make the ''hover'' circle too otherwise it'l just be square.
#elUserNav a.ipsUserPhoto { border-radius: 100%; }  

It was Selinux preventing chmodding of the directories