Yes, I know the problem well. And I don't have a good answer because it is an ingrained problem in all search engines. Basically, any search engine works on a soundex type system similar to those used for years for genealogy records. And imagine the problems of trying to soundex search genealogy records for names like Taylor, Smith and Jones.
The same problem is true with the Official Records. Commanders wrote so many reports and other correspondence that their names reoccur many times within these records. Therefore, a search of their name for example will produce many "hits".
The only answer I've found is to try to refine my searches to the least common piece of information that I know about the subject I am searching for. I sort of think of it as a backdoor method. For example if I am looking for a list of troops under Gen. McCulloch command, instead of looking for Gen. McCulloch I would maybe do a search for a regiment, like McRae’s, or some other information that I knew was in fact under his command in the first place, and see what documents turned up under that search and work back from there.
If you are not familiar with your subject matter of your search then you almost have to use the index just as you did with the old printed Official Records Books in the Library. Or wade through the numerous "hits" that you get with a broad subject search. And I know you know your subject matter Bryan.
The basic rule is the more specific the information requested in your search query is, the few returns "hits" you will get. The more you can limit the scope of your search the better off you are.
I don't know that this helps any. Again, I am no expert. The OR's just contain a lot of information in the first place.