Is there independent evidence that the Wright brothers celebrated Roosvelt's election in 1904 by a flight of over 5 minutes?
The short answer is No. The independent witnesses are missing. Only Wilbur, Orville, and possible their father, saw the Nov. 9, 1904, flight.
There exists a commented collection of old documents of the period 1903-1905 (most of them from 1904), over 200 letters and articles, all quoted in full, that studies, based on primary sources, whether the Wrights really flew a plane in 1904 (they claimed 105 landings for that year).
This book is titled: &quot;The Wrights and their impossible 1904 flights&quot;

The 1904 plane as imagined by C. Dienstbach in his March 1905 article in German (Source: &quot;The Wrights and their impossible 1904 flights&quot;, page 62)
Regarding the existence of the Nov. 9, 1904, flight, besides the letter sent to Octave Chanute, this is the evidence I could find, in the above mentioned work:

November 9, 1904 - An entry in Bishop Milton Wright's diary reads: “… I go on 11:00 car to Sims. At 2:00, Wilbur flew three (lacking one-fourth) miles in 5 minutes and four seconds. The distance was only limited by failure of engine.” (col. 1, p.28)
November 9, 1904 - Wilbur recorded, in one of his notebooks, a flight of 5 minutes and 4 seconds as the 82nd trial of that year. Orville also mentioned the flight in his logbook. (p. 95)
December 17, 1904 - The Dayton Press published an anniversary article, stating: &quot;Their work and trials have been carried on quietly. They have not made any public trial, and have no intention of making any in the near future. … The longest fights yet accomplished by the machine occurred on November 9 and December 1, when the flyer made almost three miles in five minutes.” (p. 36)
December 20, 1904 - Wilbur mentions, in a letter to G. A. Spratt (a fellow aviation enthusiast), that the longest flights of 1904 occurred on November 9th, 16th, and December 1st. (col. 1, p. 18)
December 21, 1904 - Orville Wright wrote to the German journalist Carl Dienstbach saying, amongst other things,: &quot;The two longest flights of the season were made on the 9th of November and the 1st of December. In each of these flights we made almost four complete circles and covered a distance of a little over four and one half kilometers, at a speed of about 35 miles an hour. In the flight of November 9th a weight of 50 lbs. (iron bars) were carried in addition to the weight of the operator; in the flight of December 1st, 70 lbs.&quot; The letter of Orville was published in German under the heading: “Das erste Lebensjahr der praktischen Flugmaschine”, Illustrierte Aëronautische Mitteilungen, March 1905, pp. 91-93. (p. 19)
February 3, 1904 - The Holt County Sentinel (Oregon, Missouri) published a short text that quoted the father of the two inventors: &quot; After years of unsuccessful efforts by some of the world’s greatest scientists, it appears that the Wright Brothers, of Dayton, O., have solved the problem of the flying machine. Accounts of a successful test made by them appeared in the papers last summer, and it seems that they are making rapid strides toward perfecting their invention. We quote the following from a letter from their father, Bishop Milton Wright, of Dayton, to his niece, Mrs Frank Petree. “Wilbur, on November 9th, celebrated Roosevelt’s election by a flight of nearly three miles, in five minutes, and Orville did the same December 1st. I was there. They are improving their engine and will put the experience of 1904 into a new machine by April.” &quot; (col. 2, p. 89)

In conclusion, the Press states that nobody saw a powered flight performed by the Wrights before December 17, 1904. The only possible witness (not really independent) of the Nov. 9th long flight could have been Bishop Milton Wright. However his diary just implies he witnessed the performance of that day. The father of the two inventors does not explicitly use the words &quot;I saw&quot;.
If somebody else finds new evidence, in the book or from other primary sources not quoted there, I would be happy to see it.