Mr. Scott,
I cannot speak for Mr. Certa. I have never met him, and I don't know his Japanese language level. Perhaps he misunderstood the unique counting system of Itto Ryu. Or perhaps Arisawa Sensei didn't feel it important and just showed Mr. Certa how to do the kata. In actual fact, Arisawa Sensei had such a hard Hokkaido accent that even many Japanese couldn't understand him. That is why, in the Hiden Mokuroku videos, Kato Sensei does all the speaking.
As far as the differences in kata -- they are nearly the same. I doubt an outsider watching a performance side-by-side could tell the difference. Yes, a few kata have been modified by Sokaku. However, it is the exception rather than the rule. (I will try to give you an example. Nevertheless, I have never studied mainline OIR, and my only experience with mainline OIR is the Monbusho video and the book Itto Ryu Gokui, so take this example for what it is worth.) The first kata that comes to mind is the kata called Norimi. Norimi is the 11th and 12th kata in the order of the syllabus. In mainline OIR, the defense against the final attack seems to be a suriage, whereas in Sokaku Den Itto Ryu we do a Sokaku version of an uke nagashi.
The changes may seem inappropriate to some, but I would like to point out that Takeda Sokaku was one of the last living samurai to fight to the death with a sword, and likely made his modifications based on his experiences in combat.
Sincerely,
Rodney Uhler