I encountered your second problem as well. And gee I feel relieved knowing that I am not the only one! I still remember that horrible "pause/issue-order/resume/watching-screen-spinning-while-listening-to-the-keyboard-clicking" nightmare ...

As to your heir ... hummm, was your heir the commander of that army? If your heir was actually under the command of your daimyo, that might explain it.

Also, this might sound silly, but why do you HAVE to attack Kaga with that heir? If the game glitch causes him to disappear, simply wait a turn or two, or attack with other troops.