Go in System Preferences -> Energy Saver -> Options -> Processor Speed and set it to highest. It won’t increase the render speed, but it increases the “snapiness” a bit.
As to why the update can’t find AE… did you reinstall all your apps from scratch when you switched to your G5 ? Something is wrong in the AE installation for sure.
The stall when you render could be hardware. I had this happen when my hard drive gone bad. If you get system hang here and there when acessing the hard drive, run Disk Utility and check the SMART status to see if the drive has a problem. In my experience (not with the G5 tho), RAM problems does either kernel panics or unexpected application quits, not application hangs. But if you purchased non-Apple ram, make sure it was either made for G5s or that it has a latency of 3 (CAS 3).
You might also reduce the AE image cache a bit. Often, when it’s set to 100%, it goes into VM and performance drops alot. When this happens, you can hear the system drive work like crazy.