I know your frustration! A few things that I hope might help:
First, remember there are TWO com.apple.Boot.plist files! One in your Extra folder, and one in Library/Preferences/SystemConfiguration. When I was playing with the one in my Extra folder, result were uninspiring. But playing with the other file made a big difference for me.
Second, here's what I did. I took the com.apple.Boot.plist file I attached in my earlier post, and put it in my /SystemConfiguration folder. I deleted the one in my Extra folder, repaired permissions, and restarted. If I recall correctly, that's when Chess started working. Then I copied the same file into my Extra folder, repaired permissions, and restarted. In this configuration, with the proper NV...Hal, AGPM, and GLDriver files, the system started to destroy benchmarks.
I hope this has helped. I would like to be as available as possible, as I know how maddening it can be, but my wife has just gone into labor this morning, so I might be away. If I get the chance, I will try to upload a folder of my working files for 1086, 12.2 systems. Best of luck!