Nice photograph Rapala.
I also did the stage upgrade like you did. My first issues that were limiting me was my kit lens of 70-200mm Canon with the Canon 500D body, and that was the AF and distance shots. I upgraded to the 400mm 5.6L and like you, found an instant increase in quality. The AF was not always the best though but rarely stuggled with birds being too close. Small birds are no problem, I think the only issue I had was large birds being larger than the frame. In San Francisco, I had to keep taking steps back for my first Hummingbird, although that was quite happy to wait for me to get my shot before moving on.
My next limit was frame rate of the 500D, as when I would take a burst shot of a diving bird, I would get one before entering the water and one after it left (none in the water). The new lens kept me happy for 1-2 years. I moved to 7D MkII as there was a really good deal at the UK Bird Fair a couple of years ago. This sorted out most of my issues, and I have rearranged all the buttons on the camera, allowing for me to switch to BIF mode at a touch of a button. That comes in handy as jumping from ground birds to BIF does not give you too much time to worry about settings.
That has been my current set up for the past 18 months, and do not know when it is likely to change. I tried a 1.4x convertor but preferred having the ability to use the view AF. I think my next bit of equipment is a decent computer as I make do with a laptop, which is very slow running Lightroom.
