1) Yes, this is a problem and the only way to get around it is to write your own scripts. Which you either know how to do, in which case it's simple, or not, in which case it's nearly impossible
2) Henchmen usually keep using missile weapons if you tell them to, even if the enemy is standing right in front of them getting attacks of oppertunity. To stop the charging in, give the 'follow' command whenever they start running off.
3) The size of the weapon ion your main hand doesn't matter. The one in your off-hand should be small for best results. GB already explained it.
4) The type of armour you need is mentioned in the recepy. What counts is the total armour class, so if you need an enchanted suit of armour with an AC 6, you should use a suit with AC 5 and a +1 enchantment, or AC 4 with a +2 enchantment, and so on.
5) You're not reading too much into it