Small further update, unfortunately no links on this because a) I'm still sifting through a bunch of material I found today, and b) it was all on a different computer in a different location, and I haven't had a chance to move files.
I went through the Library of Congress archive of the weekly newspaper The Frankfort Roundabout. In 1890 a note is made that one M. T. Mitchell was in the process of relocating his Old Judge distillery from Burgin, Mercer County, to the Frankfort area. In the November 28, 1891 issue, the following short item is reported:
Old Judge Distilling Co.
Messrs. Manlius T. Mitchell, Chas. W. and Henry Fincel have formed themselves into a company under the above title and have been incorporated under the Statutes for the purpose of operating a distillery and manufacturing whisky of the "Old Judge" brand. They will shortly begin the erection of a distillery near Collins water Station on Benson.
One week later, and for several weeks thereafter, a legal notice was posted in the Roundabout that contained the Articles of Incorporation of the Old Judge Distilling Co. Then, the issue of July 16, 1892, contained this item:
Land for a Distillery.
The Old Judge Distillery Co. purchased on Wednesday from Mr. A. W. Cromwell two and a half acres off of his farm lying on Benson, two miles west of this city, and will shortly begin the erection of a distillery upon it, for the manufacture of "Old Judge" whisky.
There are various ups and downs, and on July 22, 1899 the Roundabout noted "Messrs Ferdinand Westhelmer Sons, of St Joseph, Mo and Clnclnnati, Ohio, have purchased the Old Judge Distillery No 11 near this city, and will enlarge the capacity very considerably before the next season commences."
No other change of ownership is noted that I could tell, but from 1900 through 1904 or so, RD 11 is referred to as Old Judge, Laval & Mayse, S. C. Herbst, and Old FItzgerald almost interchangeably in the Revenue Assignments column. The Roundabout regularly published a list of which U S Treasury storekeepers and gaugers were assigned to which distilleries, warehouses, and rectifiers. (By the way? No John E. Fitzgeralds.)
I'm still looking at my three suspects as to who John E. Fitzgerald is. I've dismissed the gauger who was indicted in 1876 because a) he was involved in falsification of paperwork and possibly shaking down distillers for money, but was not accused of theft of product, b) he was a gauger and gaugers only carried keys to the receiving/cistern room where the new make was piped. Warehouse keys were carried by the storekeeper, which JEF was not.
There is also the possibility of John E. Fitzgerald the distiller, who began his career at the age of 17 at the Henry Shufeldt plant, and who built the Hammond Distilling Company in 1901. He lived and worked in the Chicago area for nearly all his life, and Herbst had a Chicago office. He was also active in distilling at the exact time Herbst was getting his Jno. E. Fitzgerald whiskey off the ground.
But there's a third John Fitzgerald, in Milwaukee, whose middle initial I don't know but considering that the names Edmond and Edmund run in his family, there might be a connection. This John Fitzgerald died in 1896 at the age of 63; he had been a ship captain and a ship builder, as were his five older brothers, for his entire life. His only careers were nautical, and in his old age he established a dry dock that was run by his son William E. Fitzgerald until his accidental death in 1901. As an aside, William E. Fitzgerald had a son who did not follow him into the shipbuilding world, but the family firm built and named a ship for him anyway: Edmund Fitzgerald. But the reason I'm leaning toward this
John Fitzgerald, who had no connection with whiskey or distilling at all, is because Solomon Charles Herbst of Milwaukee was active in yachting. He established The S. C. Herbst Trophy, awarded at an annual yacht race between Milwaukee and Chicago. This affinity for yachting is a very close parallel with the activity of a man whose life's work was construction and operation of sailing vessels.
We know that Herbst registered Jno. E. Fitzgerald as a whiskey trademark in 1884 and again in 1905, and there is evidence that Herbst had the Taylor distillery produce Old Fitzgerald for him when they opened shop in 1887 or so. But the whiskey...where was it sold? Exclusive ships and railroads? Not entirely.
This 1901 advertisement for Chancellor Club Cocktails asserts that Chancellor Club Cocktails (in big letters) and the genuine John E. Fitzgerald 15 year old rye and bourbon whiskey (in small text, almost like an afterthought) "are served in individual bottles in the dining and buffet cars of the best railroads in the United States" - but not exclusively, and in fact the advertisement goes on to offer the reader four quarts of the cocktails or the rye or bourbon whiskey for five dollars. A 15 year old whiskey being offered for sale in 1901 would have been distilled in 1886, which technically makes this Taylor juice - although by October 1901, when this ad ran, Herbst owned the Old Judge distillery where his Old Fitzgerald would be produced. (It also seems that he just warehoused everything until he knew he had a steady source of supply.)
So that's where my own research is up to, at this point. The exact answer may never be known (and I tend to believe now that the whiskey-stealing Fitzgerald is conflated with the story that a treasury agent and security guard were caught pilfering whiskey at a consolidation warehouse where Herbst whiskey was being stored during Prohibition, thus forcing his sale of stocks and brand, which is the "how Pappy got Fitz" story told in "But Always Fine Bourbon".)