You might want to take a look at
this sticked thread regarding installing on a Vista, and Win7 OS. It's not Win8.1, but its tips on installing the game for newer versions of Windows....newer than what's stated on the game box.
I would think installing the game into another folder other than the Programs x86 folder, would still apply. There's been a long time standing issue with games being installed into the "Programs" folder and not allowing game files to be changed, as would be the case using JSGME. I don't think it would hurt if you made your own C:/Games/UbiSoft folder....putting SH4 there.
If you have more than 3 gigs of memory, download the App
Large Address Aware to have the game use more than the default ceiling of 2 gigs of ram. This will force the game to use the extra memory your system has. The game being released in 2007, didn't expect most computers today to have more than 2 gigs of ram available. LAA opens the game to the additional memory.