#1

I liked 2 programs significantly more than the rest, although I was lucky and liked everywhere I interviewed.

definitely have a #1 and #2 - they were standouts for me. but i was also lucky; i liked everywhere i interviewed and will be ranking them all. just some places i liked more than others, obviously.
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For me there was a definite #1 and #2, that said, I would be happy to match anywhere in my top 5.

Have programs already submitted their rank lists? I know it can't hurt, but would it really do any difference if I let my number one know now?

No