Assuming I fully understood your play, you ruled correctly. If R4 had left 2B and was between 1B and 2B at the time F6 threw the ball, then the two base award is 2nd and 3rd. If R4 was between 3B and 2B, then the two base award would be 3rd and home.
I repeat that understanding because it is possible to be "headed back to 1B" but still be located between 3B and 2B, or have just reached 2B on the return at the time of the throw.
Nothing else you stated is in issue; handled correctly.
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