Me and madmatg had the same issue in MP back when it worked on .81x.

Here is the solutions we came up with:

How to get Archers/skerimishers to attack a specific unit rather than the ones surrounding it.
1-UNselect auto fire (meaning that they won't shoot unless u tell them to)
2-UNgroup them (don't have them in a group)

NOW: select of of them via Ctl+click or whatever & have them shoot. This is the only way to have ur ALL ur missiles shoot at a specific unit that is surrounded by others.

How to get cavarly (regular & skermisher) to charge a specific unit that is sorrouned by others.
1-UNgroup them(don't have them in a group)

NOW: use Ctl+click/C to select all ur cavarly units and have them attack the "specific" unit u want. (btw u need to be careful with pressing "C" because sometimes u put ur cavarly in loose formation by mistake, its just the timing of Ctl+C, so u have to make sure they get back into tight formation)

WHY????

Well missiles will shoot at WHOMEVER is closet to them. And if u have them in a group, they will be shooting at different targets when ur target is surrounded by other units.

Cavarly when u tell it to attack and the cavarly is in a group u run into trouble. IF one of ur cavarly squadrons is touching an enemy soldier from another unit that cavarly squadron will charge at that unit and NOT charge the intended target.

hope this helps