I don't know if this warrants another entry but the test program is now robust enough to handle large real world files in XML. I tried it on three 16K texts and it took 13.5 seconds overall to merge them with hundreds of transpositions. That is probably too many, but it does break up longer transpositions if it finds an alignment or insertion/deletion in the middle. The next step is to incorporate the test program into the NMerge library and thus allow the results to be displayed in the multi-version wiki.
The transposition program works in the real world and it is fast.