In checking this out a bit more carefully, I have learned that some of the BW Greek character mapping is now deprecated - at least that's how I understand it. Here is the description which I found helpful, and a table of deprecated and replacement Unicode values:
This is quoted from: http://apagreekkeys.org/technicalDetails.htmlBecause at an early stage the Unicode standard provided only for monotonic Greek and the characters for polytonic Greek were added later, the current standard contains duplication of a number of characters on the now-abandoned assumption that the tonos printed on modern Greek vowels is distinct from the acute accent printed on ancient Greek vowels. (There have in fact been some fonts that make these two accents appear slightly differently.) This is now a deprecated distinction, and it is recommended that the duplicate characters be unified under the code point in the Greek block and that the duplicate code points in Greek Extended not be used.
I contacted BW and they provided me with a text table which allows you to remap your BW Unicode Greek output. All you have to do is reassign the values in the text file, and then place that file in the BW directory. I have edited the file, and placed it in my directory, and it seems to work fine. I have not tested it exhaustively yet.
For anyone who wishes to use it, I have attached a copy of that file (bwgrk2unicode.txt). There were perhaps 7 or 8 characters that had to be reassigned. I have also attached the original file from BW, an Excel macro which will convert existing BW output, and a corrected XML file of the infinitives for verbs occurring 10 times or more often in the GNT ('corrected', of course, by replacing deprecated characters).
Now that I have files that will talk to each other - my BW output and a larger file from Perseus which Jonathan provided - I will start to work on checking output against output from different sources.