Do not worry. I am not an expert on RFE, but I have been working on rebuttal letters for tough scientific journals like CNS. You still have chance since your case was not rejected. Read the first paragraph, it is lukewarm but not negative at all. This is encouraging! You should be able to get in.
I guess you must have other membership that requires selection such as Sigma Xi since you have over 15 papers. If not, you should apply right now and rebut from the point that when you first ted I-140 you were actually qualified for the requirement rather than your recent progress. If you've already mentioned such membership, you can clearly state that such membership makes evidence that you've qualified for that item regardless of ASC.
I assume that you received your awards in the senior years of graduate school. If this was the case, you could rebut that graduate student actually works as a scientific researcher in the senior years and these awards are not only based on your scores in course study but also based on your scientific discoveries and publication.
Lots of good suggestions mentioned by others can help you dealing with leading role and breakthroughs. Not everyone earned EB1a published any CNS paper. Every paper is a breakthrough. Major or Minor ones really depends on how you described it. Let's see how many Nobel Laureates won their prizes by Nature/Science papers. Many did not.