MPG2 Muxed Nightmare. Please help me.

Hello,
I'm working in a video art project. I have a huge amount of mpg2 muxed files. More than 800 hours.
I record them using a system with no options to choose the format and I ended up in this mess.

Basically this are real time recording of entire days. Like 10 hours each and I have 100 days. My goal is edit everything together and speed it up.

I started using FCP, but the system is not happy with this kind of compression and crashes all the time. I found that Adobe premier works better but it fails to render giving me red frames.

What I want to do is convert all this files to a friendlier format DV/NTCS, H264, etc.
There is any way to convert all this in an automatic way?
I have a 2 terabytes hard drive with 100 folders(around 40 gig) with 10 or more quicktimes(about 1 or 2 gigs each one)

Converting one by one is going to take me like three months. I need a solution to convert all this files.
Any ideas?