My oldest son was a vacuum-assisted delivery and was fine. He does have ADHD and learning disabilities that were diagnosed in elementary school, but those run in both sides of our family so he comes by those honestly. I don't think there's any relationship between the vacuum delivery and his later learning issues.
As Malia B mentioned, jaundice can be caused by ABO incompatibility and is more common in a case like yours, where the mother is type O and the baby is A or B. What the doctors explained to you is consistent with ABO incompatibility.
Trouble breathing is very common, especially in stressful deliveries like your baby's. They don't just bust out the vacuum for no reason - they do it because the baby is showing signs of distress and is not handling the delivery well. Usually, the baby is "stuck" and there are concerns about heart rate and respiratory distress and this is the last step before going to a c-section. Yes there will be a bruise on the head, but it goes away in a few days.
I know that as a new parent of course you're concerned, but try to have a bit more faith in your wife and baby's medical team. From what you describe, it does not sound as if the use of the vacuum was unwarranted or a mistake or that they're "covering" for anything. You had a complicated delivery, your baby has some routine and fairly minor issues that are being treated appropriately. Just be there for your wife and baby. I would not push for a CT scan on an infant - that kind of radiation (and possibly sedation) does not seem worth it for what are routine issues following a tough delivery.
Congrats on your new baby!