Well for starters you have to use a PS/2 Keyboard or Mouse to wake the machine properly. But you may have other issues anyway, so it may or may not be trying to wake properly anyhow with your setup as you say it seems to start to try.
I can say I know for sure S3 sleep has issues on X58. Are you using the latest Beta BIOS? If not then you will have no luck anyway. I am not sure if it is fixed yet in these beta's but I do know it is not in any of the posted one at Gigabyte site
Beta BIOS's are posted in the Pinned topic at the top of this forum, and please DO NOT USE @BIOS to flash. Here is a Qflash Guide >>>