Gentlemen,
Just my thoughts as I read some of the sugggestions:
1) Crew Kills on one and two gun batteries makes since to me, it is only when you get hits on six to four gun batteries it does not. Perhaps you could kill the crew on two guns only out of six, or make them all one and two gun batteries. If you go to one shot per tube you would reduce the desire to keep the large batteries together any way.
2) Why would you have a penelty to fire out of the woods? 1000 men do not occupy the entire area of the hex (125 yards per side?) that a few trees will make it less effective to fire from. I do not like the density modifier rule you added already, I sure would not use this one either.
3) As a Union Player having all those hugh Regiments 500+ I can never stack them to the 1000 man hex capacity like the Rebs can with their smaller units. I have played modes where the unit sizes were 250 men, that was great, a lot more flexibility. In the larger games I tend to move my units stacked to gether as a collective whole anyway; it just gives me the abliltiy to face in multiply directions, move through other units, extend my line and break down to corner smaller units. All these aspects would be historical tactics.
(Key is the fire power of one 1000 man regiment would still equal the fire power of four 250 man regiments, unlike the old TS engine)
Remember K.I.S.

Lt General Joseph C. Mishurda,
"Killer Angels"
VI Corps, AoS, USA