-> 1. I can't get the image to save when I use the TiffEncoder parm to the save method.
Why do you use the Save method twice? Save method initializes saving process in a separate thread so you need to wait while the first saving process will be finished and only then start next saving process. You can execute two Save methods simultaneously only for different collections. Please see description of the Save method in documentation.
-> 2. Is there a way to maintain the tiff tags when saving the file after processing it?
Version 2.0 does not allow to do this, we will add opportunity to add, edit and delete tags of TIFF file in next version.