When you swam the 1.2 miles straight and weren't out of breath, you were swimming on the low end of the aerobic zone. So when you raced, you reached the upper end of the aerobic zone and you needed to breathe more often. That's the same feeling you want to have when you do your pace sets in the pool. Pace sets are your sets that you try to swim at race pace. Basically any time you are not warming up, cooling down, doing drills or sprinting. Sprint sets (anaerobic) are even faster and you feel very short of breath.
When I said 3 LT 3 RT 3 LT, I meant that during your stroke cycle (1 stroke left arm, 1 stroke right arm) you breathe to the left when you stroke with your left arm for 3 cycles, then breathe to the right when you stroke with your right arm for 3 cycles. When switching from left to right side breathing you would do your 3 strokes without a breath. It would look something like this: RT arm stroke, LT arm stroke-breath, RT arm stroke, LT arm stroke-breath, RT arm stroke, LT arm stroke-breath, RT arm stroke, LT arm stroke, RT arm stroke-breath, LT arm stroke, RT arm stroke-breath, LT arm stroke, RT arm stroke-breath, LT arm stroke, RT arm stroke, LT arm stroke-breath and continue.
I meant by "breathing RT then LT then RT then LT" that sometimes a swimmer's technique will completely fall apart and he/she will breathe literally on every stroke: RT arm stroke-breath, LT arm stroke-breath, RT arm stroke-breath, LT arm stroke-breath.
I believe in training like you will be racing and balanced breathing (meaning that you breathe equally to both sides). So if you race breathing every 2 strokes (1 stroke cycle), then practice breathing every 2 strokes but make sure you alternate sides (breathe to the left side for 25 yds going down the pool and then to the right side for 25 yds coming back). I practice the 3 LT-3 RT breathing technique. I once read that Paula Newby-Fraser (former Ironman champ) would train 3 strokes-to-1 breath (1 1/2 stroke cycles) but raced breathing 2 strokes-to-1 breath (1 stroke cycle). You can train 3-to-1 but you may be faster if you train 2-to-1 and go faster/harder during your pace training sessions. The 3-to-1 breathing would be fine for your anaerobic sprint sessions.