Hi lizziejt
I agree with Dancinggirl that maybe the progesterone is giving you acne? Although it is the least androgenic of the progestogens (ie the least like testosterone and therefore supposedly the least likely to cause male-type symptoms such as hair loss & acne), it is listed as one of the possible side effects so perhaps you are unlucky.
How long have you been on the new regime and how much oestrogel are you using? If you are having moodswings then it sounds like you are not yet at menopause because once you have had your last period, oestrogen levels graudally decline over the next couple of years but the hormone levels do not fluctuate as they did when in peri-menopause.
If that is the case then you could be better off maintaining a cycle as Dancinggirl suggests, and taking utrogestan sequentially. Oral HRT is more likely to exacerbate migraines. When did you used to get the migraines - during most of the combi phase (the second half of the cycle) or after you'd finished the progesterone phase and just before or around the time of your bleed?
It may well be that you don't get migraines at all on this regime.
Hurdity x