There was a suggestion today in the Help Channel to organize whispers with a list bar. I have built off it a little for these following suggestions.
Change the name of the Friends tab to Whispers in chat tabs. For that is what it really is used for.
In the friends (Whispers) tab in chat add a second bar to the right. When you get a new whisper that persons name will be added to the right. When you select there name there is a history so you can see the conversation with that person. This way you can click between the whispers and see what has been said without having to scroll back up when talking to multiple people. Have option to X close whisper from list. Have newest whisper go to the top of the list. (This will help MOD make sure they answer everyone also)
Additionally building off this:
Keep the Friends chat tab the same name. Add the bar on the right as in 1b. Not only will you get new messages, but your friend list will be shown here in the right bar. This way you just have to click on their name if you want to send them a message. Include right click send resources here and right click invite to alliance. (Offline friends will always be at the bottom of the list)
If you add the Trade chat channel by replacing the Region tab also make a right bar. People who are actively in this channel will be seen in the right bar. This lets people know they are waiting for a trade. Additionally, make it where you can right click on someone's name here to enter trade. Create a trade window between two people trying to trade resources instead of just sending resources.
In the alliance chat tab once again have the same name box of people who are in your alliance and are online. Create a right click function for Guild Leaders/officers/treasurers to send crowns from their Alliance bank to players and player kick. Also add in function to right click to send resources for anyone in alliance tab.
Have everyone online listed online in the right bar. Can make it so you can collapse (hide) bar. Have right click info, add friend, ignore and invite to alliance options here.
Example of right chat bar from another game: