I have a question.

 

When Nynaeve healed Logain she used Fire and spirit and he got all of his strength back as far as I know.

 

When she then went and healed Siuan she was thinking about how different some things are done and healed differently wether it's a man or a woman. And men, it is said, were stronger in fire and earth than women, so if she had used water and spirit instead of fire and spirit would Siuan have regained all of her powers back? Like that Aes Sedai that Flynn healed?

No. RJ specifically answered this one here:

 

For Alys Kinch, the Healing of stilling must be done by the other gender to be fully effective. A woman Healing a woman or a man Healing a man results in less than full restoration. It all ties into that theme I keep harping on. Men and women have to work together to be their most effective. And while the weave used by Flinn for Healing is not exactly that used by Nynaeve, either would use the same weave on a man or a woman.

 

http://www.dragonmount.com/RobertJordan/?p=26

Yeah, RAW is correct. X channeler that is stilled must be healed by someone of the opposent gender to regain their full strength.

ah, thank you