How is it behaving now?
Based on the log, it is finding AGP, and is using the kernels agpgart (NvAGP = 2), which is what you probably want. (it is what I use. the default is 3 which means 'try agpgart, if fail, try built in', which I don't bother since the builtin doesn't support my agp anyway.)
Are you still having problems? Any specific things to point to that look wrong?
AGP found in dmesg
AGP found, glx loaded in X log
proc reports agp enabled
glxinfo uses NVIDIA
glxinfo lists direct rendering a 'yes'
did I miss anything
Don't give up. I was almost giving up on my system, but now 3D is great. the 980 XGL is gettiing like 3000 fps, tho i think the CPU load is a little high maybe.