Im not too sure on the price. It really depends on what you have, and what you decide to go with. The difficulty level also depends on your experience and having the right tools for the job. That would most likely be a large portion of your cost if you don't have em.
As far as the difference off road goes, I can't really imagine not having manual shifting. There's just sooooo much more control. Rolling back and forth, choosing your gears, and dumping the clutch, are just the few things that come to mind first. Not to mention the maintenance factor. Manual is definitely the way to go. I couldn't live without it. I really have a hard time understanding sometimes why people would even want an automatic. But that's just my opinion I guess.