The work was very carefully done: there are about 160,000 pages of entries, and only 120 pages of errata.
The last volume was not published until 1972.
He had to invent a classification system for asexual fungi (the Deuteromycetes) in order to have a way to index them. This wasn't intended as a taxonomic system (see English for some harsh arguments he had with Cooke on this topic), just as an artificial key so that one could locate a name for the specimen at hand.
It was not completely indexed (each volume of the original has its own index) until the 1980s, under a grant from the NSF.