Hi, and thanks. Hmm… MusGlyphs is intended to correct this exact problem, so the user doesn’t have to resize and align. I find any of the typical fonts I use work nicely with MusGlyphs by default. But you’re right that line spacing can be an issue. Some of the glyphs are quite tall, so the values for WinAscent and WinDescent (basically, how “tall” the font metrics are) are set to large values. I am looking into ways to adjust this automatically, but as you can see on the MusGlyphs product page, it should be possible to make the font play nicely with text.
Also, at least on Word I know it’s easy to assign a key command to a particular font, so you can easily switch back and forth.
Regarding kerning: at least in Word, I would recommend simply turning it on and leaving it.
Updates: all “official” updates will be pushed out through Notation Central, and you’ll get an email with a link. That’s the best way, rather than relying on the Dropbox link, which may disappear at any time, or may link to a beta version that has some issues! The official version is still 1.45. The beta, 1.46, has a few changes that may throw you off a bit, which will be documented in the version history (they’re quite minor).