I am assuming this is a follow on to your posting:
Seeing / copying more lines in the serial monitor by showing the monitor on the right - Software / IDE 2.x - Arduino Forum
So I assume KiTTY is out as well 
As I mostly work with Teensy boards, I often use TyCommander:
TyTools | Niels Martignène (Koromix)
- You can select the different active com ports
- Baud rate: For teensy this mostly means nothing, as it is native USB, so baud is mostly ignored. (Except the sketch can get the value) so it can work like a USB to Serial adapter and set one of the Hardware Serial ports to the specified baud. The TyCommander does have options page on the Serial port to set the Baud rate
- Line ending yes
- I believe you can log to file, have not played much with it
- Teensy Integration - for Arduino 1.x it sets up configuration for Teensy to automatically use it for Serial monitor, It also is setup to be able to do the uploads or it can be configured to defer it back to the Teensy loader.
Arduino 2.x - Can be setup to do the same, there are instructions on this up on PJRC forum.
I do use this app for other boards as well, but for uploading/downloading and the like, I have to click to disable serial, do the upload and click to turn serial back on...