Python 2 scripts, but they do the job. Variables refer to ES2 because this is a small tweak on the original script (https://gist.github.com/brucebolt/ec211868299b8efbdde7877e9a2d3c10)

analyse.py

import csv
import re

results_es2  = {}
results_es5 = {}

with open('results.txt', 'rb') as f:
  rows = csv.reader(f, delimiter='\t')
  next(rows, None)
  for row in rows:
    for index, value in enumerate(row):
      row[index] = re.sub(r'\s*$', '', value)
    if row[0] not in results_es2:
      results_es2[row[0]] = {}
    results_es2[row[0]][row[1]] = row[3]
    if row[0] not in results_es5:
      results_es5[row[0]] = {}
    results_es5[row[0]][row[1]] = row[4]

for key in results_es2:
  found = 0
  missing = []
  for i in results_es2[key].keys():
    if results_es2[key][i] in results_es5[key].values():
      found += 1
    else:
      missing.append("{} ({})".format(results_es2[key][i], i))
  result = 'TRUE' if found == len(results_es2[key]) else 'FALSE'
  print "{}\t{}\t{}\t{}".format(key, found, result, ";".join(missing))
  

fetch.py

import requests
import sys
import urllib
import csv

print "Keyword\tPosition\tMatch\tA Result\tB Result"

counter = 1

with open('ga_export.csv', 'r') as f:
  rows = csv.reader(f, delimiter=',')
  next(rows, None) # skip header
  for row in rows:
    keyword = row[0]
    sys.stderr.write("{}\n".format(str(counter)))
    keyword = keyword.strip()
    query = urllib.urlencode({'q': keyword})
    try:
      resp_es2 = requests.get("https://www.gov.uk/api/search.json?ab_tests=search_cluster_query:A&{}".format(query))
      data_es2 = resp_es2.json()

      resp_es5 = requests.get("https://www.gov.uk/api/search.json?ab_tests=search_cluster_query:B&{}".format(query))
      data_es5 = resp_es5.json()
    except:
      continue

    max_results = max(len(data_es2['results']), len(data_es5['results']))
    num_results = min(10, max_results)

    if num_results > 0:
      for i in range(0, num_results):
        es2_value = data_es2['results'][i]['link'] if i < len(data_es2['results']) else '(no result at this position)'
        es5_value = data_es5['results'][i]['link'] if i < len(data_es5['results']) else '(no result at this position)'
        match = 'MATCH' if es2_value == es5_value else ''
        print keyword,"\t", i+1, "\t", match, "\t", es2_value, "\t", es5_value

    counter += 1