Extract PEM stuff from your file with this one easy script. Plug it into Unix find to extract all the PEM stuff from all the files.

pem_extractor.py

#!/bin/python3

import sys,re,json

PEM = re.compile(b'(?P<whole>(?P<header>(?:-----)(?:(?:BEGIN) (?P<type>(?:[A-Z]+ )*(?:[A-Z]+)))(?:-----)(?:\n|\r|\r\n))(?P<inner_base64>(?:(?:(?:[0-9a-zA-Z\+\/]{4}){16})(?:\n|\r|\r\n))*(?:(?:(?:[A-Za-z0-9+\/]{4}){0,15})(?:[A-Za-z0-9+\/]{2}==|[A-Za-z0-9+\/]{3}=|[A-Za-z0-9+\/]{4}))(?:\n|\r|\r\n))(?P<footer>(?:-----)(?:(?:END) (?P=type))(?:-----)))')

if not sys.argv[1]:
  sys.exit(1)

filename = sys.argv[1]

extracted = {}

with open(filename,'rb') as f:
  for d in map(lambda m: m.groupdict(), PEM.finditer(f.read())):
    key = d['type'].decode().lower().replace(' ','_')
    val = d['whole'].decode()
    
    if key not in extracted:
      extracted[key] = set()

    extracted[key].add(val)

for k in extracted.keys():
  extracted[k] = list(extracted[k])

if len(extracted) == 0:
  sys.exit(0)

results = {}
results['path'] = filename
results['extracted'] = extracted

print(json.dumps(results))