Don't worry about all original metal affecting the value. The value is more affected by the finished product. And you can easily keep original metal and modify it anyways.
If you're worried about value, then you might be up for disappointment in the end. Do it as you want and you'll be happy with it, value comes second, to me at least.
I'm still glad I shortened the bed. It's not really that hard, but it depends on how solid your stock bed is.
