The pertussis (whooping cough) vaccine nearly killed me when I was a child.
Take a look at vaccine adjuvants. Doctors are not scientists, they are business people, and use a lot of hocus-pocus for financial and other reasons. For a large part doctors and biologists have no clue what they are really doing.
No holistic/philosopical objections here, just pure science.
Likely you got the whole-cell pertussis vaccine which had about 10x higher rates of reactogenicity than the newer generation of acellular pertussis vaccines. The vast majority of reactions are redness, swelling, pain and not life-threatening.
The newer, "cleaner" acellular pertussis vaccine seems to be less immunogenic than the older "dirtier" vaccine. That may be contributing to the whooping cough outbreaks because it needs to be boosted more frequently than the current schedule.
Aluminum hydroxide ("Alum"), or aluminum hydroxy phosphate, work very well as adjuvants for many vaccines. They also adsorb the protein components of the vaccine and help stabilize them for a longer refrigerated shelf life.
Thimerosol ("mercury") hasn't been used in single dose vaccines since 2001. It was used as a bactericidal agent in multi-use vials to suppress the growth of bacteria if there was inadvertent contamination.
To say that vaccine developers "have no clue what they are doing" is pretty harsh. It now takes $300 million or more to develop a licensed vaccine today and the pre-clinical and clinical hurdles are steep.