As your heart rate is increasing your breathing probably is too, although it may not seem like it, otherwise you wouldn't be oxygenating the increased circulation. I think what most people miss in their training is the need to log lots of hours just cruising at a modest heart rate to build their aerobic base. As Matt said, try to spend the next 6 weeks or so spending the majority of your time around 60-70% of your maximum heart rate. You'll feel like you're not training as hard, but it WILL pay off, and quickly.