2. If you have two lines of troops engaged in a mass, contiguous combat with multiple units on both sides, do opposing units "pair up" and roll against one another one unit at a time, or is one die roll made for the whole combat?
a. As a follow-up to the above, if the losing side loses two bases per the Combat Result Table, does each unit on the losing side lose two bases or does the collective bunch lose two bases?
As far as I know, having played this rules set for a while,
1. Troops moving into hex to hex contact with an enemy unit are considered in to be in hand to hand combat, even for missile troops (although some chariot units are an exception to this, being able to fire as they charge into combat). Missiles troops who are moved into by an attacker can fire before the combat takes place
2. In a combat involving multiple units, they are paired up. If one side outnumbers the other it is usually obvious which to pair up, with the numerically superior force able to apply it's extra troops to certain pairings improving the chance of punching gaps through the enemy lines. In subsequent rounds of combat the pairings are worked out anew as the lines shift, more units join, units destroyed. etc
Hope this helps. I'm waiting for the updated rules which should make some elements of play clearer,