1. We only have known them for a short time.
2. We have only known them for a short time.
3. The atmosphere could only have been warm.
4. The atmosphere could have only been warm.
Q1) Are four sentences correct?
Q2) Is "only" emphasizing "have" in #1 and #3?
Q3) Is "only" emphasizing "known" and "been warm" in #2 and #4?
Q4) Is there any slight difference in meaning between 1 and 2, and 3 and 4? If so, could you explain?
I would say yes to three questions.
fire1 1. We only have known them for a short time. 2.
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fire11. We only have known them for a short time.
2. We have only known them for a short time.
(1) is a less usual word order. Some people may find it less natural. (2) is a normal word order. In both cases (in the absence of some very unusual context), "only" is understood to modify "a short time". The strictly logical word order for this meaning would