Stereo 3D

I'm trying to assess if Stereo 3D is something that I can potentially use. I'm having a couple of problems:
1. The Auto Align doesn't produce satisfactory results. Manual alignment, however, doesn't have enough basic controls. In particular, absence of rotation makes it really limited (unusable) as most misalignment in 3D has some degree of rotation.
2. There doesn't seem to be an easy way to slip one eye against another and it is not clear whether temporal alignment happens by time code or first frame. Either way, there doesn't seem to be simple mechanism to match the left and right eyes with a time offset.
Anyone tried using Stereoscopic 3D?
1. The Auto Align doesn't produce satisfactory results. Manual alignment, however, doesn't have enough basic controls. In particular, absence of rotation makes it really limited (unusable) as most misalignment in 3D has some degree of rotation.
2. There doesn't seem to be an easy way to slip one eye against another and it is not clear whether temporal alignment happens by time code or first frame. Either way, there doesn't seem to be simple mechanism to match the left and right eyes with a time offset.
Anyone tried using Stereoscopic 3D?