First, let me say I've never made pho.
However there is already some good advice here with regards to stock:
- http://cooking.stackexchange.com/questions/2422/should-i-roast-meat-bones-before-making-stock-out-of-itShould I roast meat/bones before making stock out of it? though I personally would also roast carrots, onion, celery with fresh herbs in with the bones.
- http://cooking.stackexchange.com/questions/2466/should-i-let-stock-cool-with-the-bones-veg-still-in-itShould I let stock cool with the bones/veg still in it?
- http://cooking.stackexchange.com/questions/2470/are-the-leftovers-from-making-stock-good-for-anythingAre the leftovers from making stock good for anything?
What are you skimming with? I'd pour the liquid through some cheese cloth, that should at least help with appearance a bit.