If you have Wye's collection of practice books [tone, technique, articulation, intonation and vibrato, breathing and scales] that should cover about everything. Or, you can get them in the one volume edition [Omnibus edition books 1-5 entitled: Practice books for the flute by Trevor Wye].
Basically, these are a new spin on a lot of the taffanel and gaubert studies.
As for tone studies routines, you can use about any of his excercizes on a daily basis. But, I would focus on one register at a time. [lower for about 2 weeks, middle for about 2 weeks, upper for about 2 weeks, then repeat the process]. Or you could do the excercises that are helpful regarding the piece you are working on right now.
As for technique.... about anything in the technique book will help. Just work on your weak spots.
Although it is very pervasive, I don't really like the distinction between tone, technique, articulation, and so forth. I think of my practice as being made up of the three major sections--scales and arpeggios (includes T&G exercises, etc), etudes, and repertoire and excerpts. This works for me since I know what I'm trying to do when I'm practicing something. I'm not really sure what I would do if I had to practice *just* tone for 45 minutes.. I think it's best to think specifically about what you are trying to improve and practice whatever addresses those things. Other people's guidelines can be helpful, but don't take them too strictly. Everyone develops their own way of practicing over time.
I do think that scales/arpeggio exercises are really the foundation of flute playing and that everyone should include some in their practice.
10-15 minute warm up (which would be the memorized technique portion)
30-60 minutes on T&G
30 minutes on etudes
30 minutes on solo repertoire
I have been playing out of T&G but I'm taking the exercises slow, most at 60bps to the quarter note when the exercise is in 16th notes, but there's a lot that the book covers, so I'm sure it will all fall into place if I keep learning it steady and consistently. (It would be interesting to have a topic up on how people are progressing in T&G since there's so much in there!)
The main reason I brought the topic up is because I have a hard time with some of the high notes past E3. It's probably more of an issue of my playing rather than the flute, but I'm not really sure. I just don't like how the upper register sounds on my flute. It sounds really harsh and it's just as hard for me to play in the upper registers on some notes.