I think I found a system that works! I am not doing the database after all, because that is still a lot of time spent on meta-writing, which could be time spent on writing. Here is what I came up with instead for doing my rewrites:
Step 1. Print out the chapter with all of the inline critiques. Chapter 1 clocked in at 37 pages doing this.
Step 2. Go through the whole chapter, deciding which critiques to work in and which to ignore.
Step 3. Go back through the whole chapter again. This time working in MY changes, sometimes overriding what I just put in from the crits. (Oh yeah. Somewhere around step zero was putting the whole story on my kindle with the paragraphs numbered so I can take notes while I read)
Step 4. This was the magic for me. (IMHO, anyway) I break the chapter into scenes. Separate file for each scene.
Step 5. Print out one scene, latch it onto the clipboard, and focus only on word selection. No story telling, as that is already done. This is where I go through and remove weak words and phrases.
Step 6. Recombine the scenes into a chapter.
YAY! I think that it results in a much better piece of work. I guess I will find out when it hits the critique site. With any luck, both of my loyal readers will let me know what they think!
So there it is. My system. Still interested in what others use for their editing efforts.