ToddyWood,
Ignore half the people on E.T. They are just mean at times. I am not sure exactly what would be causing the slowdown but there are a few things that may or may not help. Make sure Audio is not the problem. Take off sync audio to game when it slows down to make sure it's not audio. You can also try using HLE Audio instead of LLE. The problem I think you face is just the whole graphics HLE process. When there are many polygons on the screen, the HLE Graphics plugin will take a large percentage of the CPU time. This has nothing to do with your graphics card. A suggestion could be to lower resolution in full screen, or perhaps try a less accurate plugin that plays CBFD. Jabo's plugin is great, but it is slow because of its accuracy. There is no way around that unfortunately. My ideas probably won't help, but if anything, I hope it puts a virtual bandaid on the wound so you don't feel you can't ask for help.
Oh... and WinME is bad. You should go with 2K or XP since they are much more secure and you have the RAM for it. Also, make sure you close down anything unnecessary that may be causing the ROM to swap to virtual memory. CBFD is one of the largest roms (64MB) and it probably has a proportionate amount of code cache required.