Hey, I started working on my plexbox again today, and the fan on the GPU is in my way. Things inside are getting really tight, and removing the fan (so it doesn't click against cables) is pretty much my only option. Is this safe? In the later xbox versions they eliminated the fan...Is this because it was un-necessary, or was the gpu improved?

The GPU fan on the version 1.0 X-Box's was a bit of an overkill. I think M$ was worried it may overheat.
It seems it wasn't necessary, thus M$ did away with it on the version 1.1's and later versions.
Provided you use the same type heatsink as the V1.1's or higher versions instead of the V1.0 heatsink/fan combo you shouldn't have any dramas.
Don't be tempted to just remove the GPU fan and use the heatsink on its own, as it won't be adequate enough.
Regards,
DarkMatter

Just put a fan guard on it....

Just replace the CPU and GPU heatsink with iceberg pros.

Just replace the CPU and GPU heatsink with iceberg pros.