that would appear to be the same shock i put in mine so i can say it should work, others have as well, i used one off of a 00 750 which should be the same as yours
what i did, and mind you this method takes some time, basically lots of trial and error, but I'd stick the shock in and just stick a bolt through the top most mount so it stayed in the bike and try and line it up with the bottom mount, i'd look and see where the shock and linkage contacted each other stopping them from lining up, take it off and grind that area a little, put it back in the bike and repeat, it took literally probably 20 attempts and each time when i removed material from one area it would get closer to fitting and then it would contact in a new area... but that way you don't remove more metal than you need to and not in any wrong areas
maybe its just the photo, but it looks like you took a brillo pad to your shock linkage, mine looks like a maniac went at it with a chainsaw, and like I said i only removed just enough to make it clear, so I think you just haven't taken off enough material yet. All in all i had to grind some off of the bottom shock mount itself, the front of the shock's bottom spring plate, i had to grind down the entire top of the shock linkage, as well as grinding a notch between the bearings... also i had an issue where the airbox kept the shock from rotating forward enough to line up, but if you've removed that then it shouldn't be giving you any problem