1- should never be of an issue. Powder just means less time necessary;

2- if you did not add acid yourself, no issue here either;

3- only experiments can tell and is my proposal.

0.4 of 10x extract should resemble 4 gr rue and should be fine. In glass of water is OK.

Boiling: if you do not run a pot dry, you cant screw up a brew actually.

I cant see you made a mistake anywhere in the process.

It's still possible to have had an occasional intestinal confrontation act once of a kind. If I were you I'd check first 0.2 of the rue extract solo. If ok then on another day check 0.4 of the extract solo. Then you know at least something.