The things about leaving the isos alone is that when I play it in XBMC it loads up the whole cd along with the menus, trailers, and FBI warnings (bah). Plus, XBMX marks all the episodes on each iso as seen. (Not sure if they fixed this issue with Dharma.)
In addition, I plan to turn it into a server. Having multiple people accessing the same iso might cause performance issues. I know this is very unlikely, but like aequalszero mentioned, I am a perfectionist.
I wanted to use MakeMKV, but have found that I can't automate it. At least, I'm not sure how. The GUI only lets me load one iso at a time. The CLI seems more powerful, but I can't figure out how to use it. What I would like for MakeMKV to do is to go to each iso file and do it's thing, but output the mkv files to same address path, except on a different HDD. (C:\\iso path* to D:\\iso path*). Then I was going to use bulk rename utility to go thru each of the mkv's and rename them to S0?-E??.
For now, I'm going to try to unpack the iso and see what kind of challenges that presents. I'm learning how to batch/script to automate all this stuff.
So far I learned how to copy the file structure from one HDD to another using the DOS XCOPY command. Whew, this post is longer than I thought. I'll keep writing on this post, just in case someone in the future is stuck in the same or a similar situation. Thanks!