I have been going through this same question, here is what i can come up with.
1- The 400mm is primarily a birding lens, the 300mm can double up as a sort of marco, and general long prime lens. As your username is BirdBoy i am going to assume this is the primary use, and for that reason i say that the 400mm would be the better choice here.
2- According to what i read the IQ is not as good when the TC (1.4x) is attached, drops slightly but still lots of people use this combo.
3- It will retain auto focus with a 1.4x converter.
4- Depends on your usage, 400mm 5.6 if its going to be for birding almost exclusively, if you need something a bit more versatile then the 300mm will be the better option.
I am going to go with the 400mm 5.6 because my primary use if birding, and as always gets said in here "Alway go for the longer glasss even if its slower for birding". I have never used an IS lens so far, i am sure it would be useful, but i want to go for a focal length as long as i can.
I am also going to get the 1.4x conveter for it, it might auto focus with the pin taping trick, if not i would have to manual focus, but its the cheapest way i know to get to 560, and apparently it drops very little in IQ.
Hope this helps a little bit with your decision.