I found myself worrying about Fawkes halfway through this chapter, but thinking 'oh, now that Harry has him, he should be fine.' Excellent!
The only real issue I have here is the same one I usually have in stories where a phoenix becomes attached to Harry - and that's that Hedwig still needs to get attention too. Lots of people solve this by turning Hedwig into a phoenix (usually a white one), but I think it's more interesting if he has competing loyalties. Since you've already got a bit of that (in the Harry vs Hermione vs Luna thing), it should be interesting to see where you go with this.