One thing that I might point out is that Jesus could, in fact, have said it the way he said it and meant water and spirit to be two seperate events. However, as you pointed out, he would more likely have said “of water and of spirit.” Protestants seperate the two because otherwise it casts doubt on their understanding that baptism and salvation are two seperate events. However, the Bible does not teach this. The best evidence for this is 1 Peter 3:21: *“Baptism, which corresponds to this, now saves you, not as a removal of dirt from the body but as an appeal to God for a clear conscience, through the resurrection of Jesus Christ” *A Protestant will likely object that the verse says, “not as a removal of dirt from the body.” “See,” they’ll say, “it’s the ‘appeal to God for a clear conscience’ that saves you.” However, a competent reading of this verse reveals that it very clearly teaches the Catholic position on baptism. First, see that it teaches that in the resurrection of Jesus Christ we can hope - not just for the forgiveness of our sins - but for a clear conscience (rather than throwing a cloak over our sins, God gives us a clear conscience). Second, take out the core of the verse (the subject, verb, and object): “Baptism saves you.” Can it get any clearer than this?
The Catholic Church insists upon using scripture to interpret scripture, and since 1 Peter clearly says that baptism saves us, then when you go back to Christ’s statement to Nicodemus, it makes more sense to see him as talking about one event.
As for the interpretation that the “water” is the amniotic fluid, the best thing to do is to find whether there is another example in scripture of the word “water” being used (in the same way Jesus uses it) to refer to amniotic fluid. I may be wrong, but I don’t think there is any.