Can I join the legion and do the Civil War quest line AFTER completing the main story?

Solution 1:

Yes.

I've done this succesfully. The main questline was one of the first questlines that I finished (mainly to get the Dragon Shouts exclusive to it), and the Civil War questline (the Imperial Legion path) was one of the last questlines I finished (because I can't decide who to support, initially).

A word of warning, though: There are a few bugs associated with one of the main quests, coming from a variety of questlines, including the Civil War questline.

If you do not trigger these bugs, or have done a workaround, you should be able to complete the Civil War questline even after the main questline has been finished.

More info:
http://uesp.net/wiki/Skyrim:Main_Quest
http://uesp.net/wiki/Skyrim:Stormcloaks
http://uesp.net/wiki/Skyrim:Imperial_Legion