I copied the simple phpinclude from the speedy and working default template and it seems to be fixed! Now, to try to isolate exactly what piece of code there is slowing things down...
I only have two things in there, the template version of the front page avatar hack, and a call to the thumbincluder relating to Photopost. I'll report back.
You are my hero, Xenon!
[high]* Alien is NOT worthy!
[/high]
-Jason