There is an older post with the VR Missions complete to 99.4% but the 3 missions remaining were frustrating to complete.
I tested my save on a new account and after I completed the first sneak mission Virtually Impossible popped. I suggest completing all of the other MGS2 achievements prior to using this - "Great Dane" might be the exception.
*Credit to BD132 for the original file that was at 99.4%
1. This is for the US version with VR mission complete to 100%. There are a few posts on how to use this file on the EU/PAL version in the Great Dane thread.
2. Rehash and Resign/replace your file
3. Complete any VR mission