Wow, wow, wow! I finally beat the game (too bad I had finals that disrupted my playing, and on top of that I had to go to Toronto for the weekend), and the whole final part was amazing. I had a hard time against The Boss at first, especially since I tried following Zero's advice at first (hide in the bushes, sneaking up on her, etc.). But I finally started just countering her CQC and punching and kicking her to knock her down and then administer a shotgun shot to her head. It took 16 of those to finish her off. But too bad the cut-scene afterwards had a different camo than the one I was wearing.
The phone call got me a bit confused though, especially since I had subtitles set to off.
BTW, you can't leave Eva behind. The action button doesn't work anymore, so you can't get over any obstacles, and if she dies, it's game over. I would like to know, though, what choosing the wrong weapon at the end does (I heard you get an extra weapon for your next playthrough?).