Compression readings

"It" -being the head...doesn't have a compression ratio..but we know what you meant.lol

It's safe to assume one head had maybe .015 more milled from it than the other .
You should always cc a single replacement head. If they aren't a pair from the factory, and sometimes even if they are, they will be different. I've had one chamber by itself be 4cc smaller than the other 3 with a set of J heads. It shouldn't really run rough per say cause of that...but maybe the vj leaks or it's a drastic flow difference..some do more than others at machine shops. Some just touch the 45 and send it, others might do a deshroud.. who knows.
What is was concerned with is intake manifold to head alignment, could that be a issue.
I would say your correct one head was milled more than the other, especially that I had to replace one which was cracked, which I found before the engine was even started.
My only question is would you pull the heads and send them out to get CC all the same and have heads checked for differences in resurfacing?
I really feel the none of the valves is leaking, its just a difference with milling
Thanks