I would like to point out that while all clone/summon/puppet are % of original's stat:
Not all % are equal. Kankuro vs GNW kankuro, for example, I believe is 60% vs 80%.
base stat distribution are not equal: so your fire main clone takes less damage than your sage naruto clone, but what is the damage ratio between your fire main and your sage naruto?
Note that damage taken is not linear to defense value. So if your sage naruto, for example, takes 20% more damage than fire main, then it might be normal for the sage clone to take 50% more than the fire clone.
Also, how many test run did you guys do? I'm sure you know there is some damage variance in damage. You need to track the individual damages, the mean and the standard deviation to see if you are within 5% alpha.