at first i didn't think it was working until i watched your video, then i saw you using the wet/ dry amount what ever it is, i'm also having simlar issue with some parts are aligning some are not, thanks for the video.
I still dont get the align takes tool to be honest. hopefully you could post an update about where your findings take you. also have you tried MK Slicer? perhaps youd have better results there. Cheers!