Pumping 2-4 ounces is a huge amount. Remember your baby's stomach is a little bigger than a golf ball. That is why babies need to eat small amounts frequently. The amount you can pump does not equal the amount a baby gets. A mother can be exclusively breastfeeding and her baby and she may be able to only pump less than an ounce. You can't tell how much a baby gets by how much you can pump. However, since you can pump sooo much you can be confident in your ability to make milk.
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It's normal for your nipple to look smashed. A baby doesn't have to be perfect at breastfeeding to be able to breastfeed.
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It sounds like you are so busy with pumping and trying to diagnose how he is nursing that you aren't believing in your and his ability to breastfeed. It's normal for your nipple to look a little smashed. It's normal for a young baby's latch to not be perfect. Frequent nursing can build supply better than long nursing. Nursing for an hour may be too long.
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A baby can't regulate intake with supplemental bottle feeding. The baby may nurse and then suck a lot down from the bottle even if they don't need it. That can make them gain too much weight and have digestive problems.  If your baby is gaining 4 ounces a week (1 pound a month) then he is getting enough. He may have other physical issues that can't be detected or that show up later.
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The only time my breastfed grandson didn't cry was when he was on the breast. He cried until he was almost a year old and started walking. He still cried and fussed much more than normal. It turned out he is allergic to everything. He tests allergic to peanuts, wheat, eggs, chicken, beef, & pork and that's just the foods. He has had head to toe eczema since he was around 6 months.
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Some babies just seem not satisfied. Try to relax, meditation can do wonders. Babies get stress hormones through the milk. Your baby may like massage. Lots of skin to skin contact can help. Try to move towards enhancing the symbiotic relationship rather than relying on pumps, drugs, and manipulating feedings.