I've poked at Jutoh pretty extensively, but I've never actually published with it. I did my last book with Vellum. I'd say they're kind of polar opposites.
Vellum imports your word document, splits it into chapters, and strips absolutely everything out of it other than italics & bold. It autodetects scene breaks and replaces those with a Vellum scene break which could be the ubiquitous *** but could also be a line or graphic of some type. It automatically reformats the first paragraph in a chapter and the first paragraph after a scene break to a different style (drop cap, no indent and/or different font or small caps). You pretty much just pick a set of formatting presets and then go through and make sure it detected everything correctly. On the other side, it's pretty much a take it or leave it. It has a few dozen options and it limits you to those.
Here's an interesting tidbit on Vellum. All graphics are transparent and remain transparent if you reverse the background or make the background different like parchment on a color device. As most people know, these devices don't support transparent PNG graphics, but Vellum's built in graphics are XML vector graphics embedded in the CSS. I don't read on a tablet often, but when I do I always turn the background to parchment so this was very cool.
Vellum also, fwiw, automatically puts your body text into Palatino as an author font for Kindle rather than leaving it as the default caecilia. Users can change the font, but if they do, it will change the different font used for drop caps, chapter titles, and first paragraph after chapter/scene break. I think it actually produces a nicer looking but, but it kind of annoyed me because I'm a big caecilia fan in terms of readability of the font on an e-ink screen.
Jutoh is more of a hands on editor. It imports your word doc, breaks it into chapters, and generates a TOC. Other than that, everything is in your hands. If you don't want it to use the formatting you had in Word, you need to reapply styles to everything otherwise its going to leave the word styles and pass on the extraneous HTML into the epub. If you want to change *** to a graphic, you need to do it yourself and you need to have a graphic for the purpose to import and you're going to need to do it for every single ***. I'd guess it would take a couple of hours to format something in it. If you're not familiar with working with styles, there might be a learning curve.
I haven't had any issues with Yosemite. 2012 MBA 11 updated from Mav to Yosemite and a 2013 27 iMac that was a fresh Yosemite install.