The answer is probably hard manual masking work for each and every of your problems because based on your description we only can conclude that it was shot wrongly in teh first place. You might try eliminating black fringes with the Remove Color Matting effect, but for your other two problems you will really have to spend some time drawing and animating masks frame by frame. And rrather than looking for easy solutions with tracking that's probably what would have worked better in the first place. Anyway, without seeing a reference shot it's impossible to advise specifically.
If you have accurate animated masks using Mocha, try precomping them to use the results as a track matte for a solid, which you set to the Color blend mode. To change the color of the shirt, change the color of the solid.
If it doesn't work, you're not out much time, which you can then use to ponder Mylenium's always-sound advice.
I am also still rather new to After Effects on a whole, so i hope this is not the wrong information, but check out this four part tutorial from Andrew Devis:
(dont forget the other three parts) - In this series, he explains some great tricks to remove lines and clear spaces around masks. He also provides some great Keying sites that may be used for practice.