1. Player A plays Elan, which states that after his turn, he must reshuffle the discard into the deck. Player B then plays Counterattack, which allows you to mimic the last card played. However, there is no discard pile and Elan is back in the deck. Does Player B still get to mimic Elan?
Yes, Elan was still the last card played.
2. Player A declares a combined arms attack (foot artillery and line infantry) with two units side by side on a hill. They are attacking an enemy unit (French light infantry) which is downhill and in between them. Can the foot artillery support the line infantry in the combined arms attack even though the artillery is technically within melee distance of the enemy? Or must there be at least one intervening hex of distance between the artillery and the enemy unit?
Yes the infantry and artillery can still perform a combined attack, irrespective of it being in melee position.
3. Player A activates two adjacent units that will be conducting ranged combat against an enemy unit with an attached leader. The first attacking unit fires and rolls a retreat symbol. Can the defending player choose to NOT use the leader's "ignore one flag" ability, take the retreat, and thus move his unit out of range of the second active unit? In short, can one "ignore the ignore?"
Yes. A leader may ignore a flag, not must. It very well may be prudent to take the flag instead of staying and being shot to hell.
You're right, it's a great game. Have fun.