About the tilde: Apparently the ~ is taken in its usually meaning, not as literal ~. I get a Package pdfpages Error: Cannot find file `test\nobreakspace {}it' error for a test~it file. Taking the filename verbatim should help. This can be done by \Verbdef from the newverbs package:
\usepackage{newverbs} % ... \Verbdef\filename{C:/Users/MYUSER~1/AppData/Local/Temp/mypdfpdf.pdf} \includepdf[pages=-]{\filename}
It is also possible to write \string~ instead of ~ every time. You shouldn't use math symbols to "escape" these characters in filenames. Typesetting and file reading are two completely different things.
Finally you can use the e-TeX primitive \detokenize{...} to sanitize the file name:
\includepdf[pages=-]{\detokenize{C:/Users/MYUSER~1/AppData/Local/Temp/mypdfpdf.pdf}}
To allow spaces you need to wrap the filename in " ". At best you should avoid any spaces, tildes or any other special characters in filenames.
\string~for the tilde and enclosing the whole file name in a pair of double quotes"for the space.