Ryan, I've never tried uploading the raw MP4 files the GoPro spits out. Since I always need to cut something together, I have only uploaded the WMV files that I encode out of Windows Live Movie Maker. It comes with Windows, or you can DL it from Microsoft for free if you are running a valid/legal copy of Windows. It's certainly not the best out there, but it's easy to use.
As for other programs, you'll have to find a video editing forum, or ask Google, as I've never used anything but WLMM. I'm sure you could torrent a copy of Final Cut Pro if you looked hard enough though. On this same topic too, hope you have a decent machine to run all this on, since HD transcoding is extremely processor-intensive when you finish editing and ask the program to spit out a complete file you can watch or upload to the Tubes, you will want to be running nothing else while it's thinking. Some of the 10 minute HD WMV files can take an hour or so to transcode, FYI.
As for uploading errors, try using the Java powered "advanced uploader" or whatever YouTube calls it. you must have Java installed on your machine though, which is free. This uploader has the ability to resume in case your connection is interrupted a little, or if there is a hiccup on their side. Having a fast, non-wireless connection is always a plus too, since it's less prone to interruption.