Well, I already "completed" the 40-day meditation this way with all of the chakras.
Are they technically opened albeit weaker? What % weaker will they be?
Can I recover my mistake by restarting and doing it properly, or is it too late?
If you can feel your chakras they are open.
Start doing the full chakra meditation which you can find at ToZ, and than you can experiment which chakra is weaker. Work more on the weaker.
Cleaning, empowering protecting, do these three and you'll be good. There is no permanent power loss because you did the opening like how you did. One could open their chakras with only yoga too.
It really is just about empowering and cleaning the chakras, and they open by themselves. The Opening The Chakras meditations are there to flow some energy through the chakras, so they get used to it.