I don't find either version particularly idiomatic. Sometimes there's no way to avoid using Perfect forms - but example #1 has three unnecessary instances.
Example #2 is in some ways even worse, because it introduces a Simple Past form (we were surprised) into a Present Perfect context (you have told us, it has been raining).
Finally, I don't think this is a suitable context for using even if instead of although. As a general principle, we only use the construction even if [Assertion 1], [Assertion 2] in contexts where [Assertion 1] is a possibility (which for the sake of argument the speaker is willing to concede might be true). In OP's example it simply doesn't make sense that the speaker might be referring to the possibility that he might have been forewarned - the whole point of the entire utterance is based on the fact that he had been forewarned.
Therefore I suggest that to fix the "basic syntax" we'd need something like ...
Even though you told us before, we were surprised because it has only rained a little.
But to be honest, even though I'm not sure exactly what OP's utterance is supposed to mean, I don't think it's something a native speaker would ever say. Taking a wild guess at the intended meaning, perhaps...
Although you warned us [to expect dry weather], we were surprised how little rain there was.
(In any context I can reasonably imagine, the speaker would probably place exaggerated heavy stress on one or more of the words were, surprised, how, little, rain.)