Please take a hard look at all multi-wound units. MW units in this game have a huge advantage over others. They are not as affected by battleshock to the degree like single wound units. Also, you might look into putting in size caps for units. That could be used as a balancing factor as well. Large units of MW models are ace in this game.
Also, how are you playing summoning? In our club we have a debate currently as to what you can summon and what you can't. Some of us believe that you can't summon a unit unless its warscroll is already in play, ie, the unit is on the field. Others think that wizards have all of the summoning spells from a faction, regardless if the unit is present or not.
I believe that if a warscroll is not in play (ie the unit is not on the table), then its summoning spell is not granted to the wizards. The logic behind it is this:
A wizard warscroll states which spells it has. A unit's warscroll that can be summoned grants the spell to the wizards. Therefore, if that unit is not in play, then you don't have that warscroll, and thus you don't have it granting the spell.
This is just my interpretation, but it seems logical and also limits summoning. Coupled with the fact that each wizard can only attempt a spell once keeps models like Nagash from going crazy.
Nice job on trying to wrangle this thing. Don't get discouraged.