Your initial assessment revealed an apparently healthy, normal, transitioning newborn. Spitting up a small amount of bloody fluid is NOT abnormal in a newborn, whether C-section or vaginal delivery. Remember that until a few hours ago, the baby was living in a fluid-filled environment with fluid-filled lungs, and that he probably swallowed a few mouthfuls on the way out. That is the most likely source of the baby's secretions.
In a low-risk mother baby setting, we are forced to rely on the parents to notify us promptly of changes in the baby's condition. If the child had been overtly cyanotic and gasping for breath, I'm sure the parents would have noticed and called for help. Most call for every little thing; few overlook obvious signs of distress. I suspect that you witnessed the early changes in the baby's condition, otherwise the parents would have been screaming for help in the hallway.
Now, on to your questions: The 7cc of bloody fluid pulled from the baby's stomach was most likely swallowed amniotic fluid and blood from delivery. Pulmonary bleeding, if it occured with the pheumothorax, would not likely be swallowed by the baby. So please don't worry about that. Pneomuthoraces (sp?) can occur spontaneously in otherwise healthy newborns, and are often discovered incidentally when chest x-rays are taken for unrelated reasons such as suspected fractures. They usually resolve with little intervention other than comfort and support measures and rarely cause any long term effects. There is nothing that you or the parents did to cause the pneumo, or could have done to prevent it.
The baby's poor color was likely due to cold stress as much as poor oxygenation. An O2 sat of 60% is certainly not desirable, but given the prompt attention the baby received, not likely to cause any long term problems, either. Remember that in utero, the fetal paO2 is only about 35. Neonates' brains and other organs are used to living in an oxygen-poor environment. Brief periods of oxygen deprivation in the immediate newborn period are not usually harmful in the long run.
The only thing I can suggest is more frequent monitoring of baby's temp. The need to assist newborns in thermoregulation is something most parents don't understand very well. They are often eager to undress and inspect the baby, which is fine under a warmer, but not OK in a cool room. They adjusted the room temperature to their comfort level, not understanding the baby's needs. Becoming hypothermic can have a cascading effect of complications in a newborn: Cold stress---increased glucose utilization---possible hypoglycemia---burning of brown fat---buildup of metabolic acids---increased demands on respiratory system---s/s of respiratory distress.
So, the simple act of maintaining warmth for the baby can help to prevent a number of possible complications. (Although the pneumo would have happened anyway, so don't beat yourself up over it.)