Yes, definitely continue with the 3 pumps per day. It's going to take a bit of time for your body to adjust. I always found the Oestrogel seemed to give less of a dose towards the end of the canister so I used to start a new one a bit before the old one ran out so I was using one pump from the old canister and other pumps from the new one to ensure I got a stable dosage. HRT is not a magic cure - it takes time and patience to find the right balance and you are lucky to have a doctor who is clearly trying to get you sorted.
Good luck Dg x