Permissions for Applications folder

I think that my permissions in the Applications folder are not right. I first noticed this when trying to upgrade/update software. In the past, I've just dragged and dropped the new software to the folder, where it replaces the old software. I get a dialog asking if I want to replace the item, I say yes, and that's that. Now, I get the dialog asking if I want to replace, but it is followed by a message saying that I don't have sufficient permissions.
I can manually drag the old item to the trash and delete it, then drag the new item into the folder. This makes no sense to me and I would like to be able to just replace the old with the new as I did before.
Checking the permissions with Get Info I see that I am designated as one of two "everyone" groups and I have "custom access". All of the items within Applications shows 4 groups/names:
everyone (custom)
system (read write)
admin (read write)
everyone (read only)
Yes, there are two "everyone" with different settings. I haven't figured out how to tell what the custom settings are, but there is a notation that "You have custom access".
I have tried manually resetting permissions for the entire folder. That didn't work. It appeared to be changing permissions, but nothing actually changed.
I tried logging in as root, but found that even there I could not delete any names/groups or change permissions for items in the Applications folder.
Questions:
Shouldn't I have full access to everything as root?
How do I change permissions for items in Applications so that I can replace them without having to manually drag items to trash then manually drag the replacement into the folder?
When did Mac's permissioning become as arcane and convoluted as Windows?
Sorry, ignore that last one. This has been a very frustrating journey for me.

Thank you! That worked. Here's the report:
I issued the Terminal commands you suggested in the other thread you linked to.
I then ran Disk Utility's Repair Permissions. It took about 30 minutes and returned 799,331 legitimate permissions errors, which it fixed. All were in the Applications folder.
I ran Disk Utility again and got no permissions errors. I did get some ACL errors in:
ACL found but not expected on "private/var/root/Library/Preferences".
ACL found but not expected on "private/var/root/Library".
ACL found but not expected on "private/var/root".
ACL found but not expected on "Applications/Utilities/Disk Utility.app/Contents/Frameworks/DUSupport.framework/Versions/Current".
ACL found but not expected on "Applications/Utilities/Disk Utility.app/Contents/Frameworks/DUSupport.framework/Resources".
ACL found but not expected on "Applications/Utilities/Disk Utility.app/Contents/Frameworks/DUSupport.framework/DUSupport".
ACL found but not expected on "Applications/Utilities/Disk Utility.app/Contents/Frameworks/DUSupport.framework/CodeResources".
ACL found but not expected on "Applications/AppleScript/Example Scripts".
ACL found but not expected on "Applications/QuickTime Player.app/Contents/Frameworks/DotMacKit.framework/Versions/Current".
ACL found but not expected on "Applications/QuickTime Player.app/Contents/Frameworks/DotMacKit.framework/Resources".
ACL found but not expected on "Applications/QuickTime Player.app/Contents/Frameworks/DotMacKit.framework/DotMacKit".
ACL found but not expected on "Applications/QuickTime Player.app/Contents/Frameworks/DotMacKit.framework/CodeResources".
ACL found but not expected on "Applications/iTunes.app/Contents/Frameworks/iPodUpdater.framework/Versions/Cur rent".
ACL found but not expected on "Applications/iTunes.app/Contents/Frameworks/iPodUpdater.framework/Resources".
ACL found but not expected on "Applications/iTunes.app/Contents/Frameworks/iPodUpdater.framework/iPodUpdater" .
ACL found but not expected on "Applications/iTunes.app/Contents/Frameworks/iPodUpdater.framework/CodeResource s".

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