Are you sure? Haha, I mean, you're right about "all sorts of hell going on" but is it really this bad? If it's normal, then I think I can live with it, but it's kinda funny, my car sounds broke as I decelerate.
Anyhow, I dunno if you flexed the input shaft as much as I did. I think at one point in time the input shaft was not centered in the bearing retainer ("candlestick"?), there was so much pressure on it that it was closer to one side. As soon as the engine was seperated though, the input shaft seemed centered, and unharmed.. But I hope I didn't harm an internal bearing.
I think I will make a video tomorrow and see if I can post it up, just to make sure the sound is normal.