Hmm.. I like it. HOMM in warcraft. but I don't think it's an easy thing to do such a game into one map. Especially if it's gonna be multiplayer. I have thought of doing such thing but many things made me think otherwise.
Before you read the rest of my reply, please note that I have only played HOMM 5 & 6, so I'm not sure if what i'm talking about will also be also the same with your situation
First thing I thought that would be hard to recreate is the movement system, how the pathing would work, how the estimate of the "days needed to go to the destination" (The one that is displayed near the mouse before you make a move) and how you could detect where the mouse is.
What I thought to be the solution:
For the movement system, estimation and the movement limit, you could replace the move command with a spell (targets ground or units) so that when the player targets the ground or another hero, you could detect the distance of the hero unit and the target point and get the days or movement it takes to get to that point. If it doesn't exceed the movement limit of the hero unit, order it to move to that point.
Next problem would be the town tier and the building tree.
What I thought to be the solution:
Make a spot on the map and use it to make the building tree. Whenever the player "presses" a button on that building tree, you level up the town.
and another problem would be....err.. wait, I just realized that your only problem is about the stacking and the damage etc.
Well, the only possible way I think this could be done is by triggering the damage, health and everything. But it would not be efficient. You can show the number of units in the stack, the damage, attack, health etc in a multiboard. If the unit stack is selected, hide the multiboard of the last selected unit and show the multiboard for the selected unit. When a unit attacks, you can calculate the number of stacks and damage (NumOfStack x Damage) and deal it to the target stack. I'm afraid that you'll have to trigger everything to make this work smoothly and without any lags in the map. and AFAIK, custom stat system will not work for this purpose.
Sorry for the very long reply. I just love HOMM :3