In makepkg, the following code is too weak.
---
$FTPAGENT $netfile 2>&1
if [ ! -f $file ]; then
error "Failed to download $file"
msg "Aborting..."
exit 1
fi
---
On most time, wget get a partial file, and makepkg assume it is full package.

I suggest there should deal with three thing.
1. Whenever FTPAGENT return code is not 0, think it is failed
2. When all files download, also touch a file 'src/download.done' that means all file have successful download. The makepkg can skip download when it found the file.
3. There should have a method to deal with partial download on /var/cache/pacman/src, I suggest that could be done by touch a file eg. /var/cachce/pacman/src/gcc-4.0.2.tar.tgz.done to do this.