//Its currently implemented really weirdly because it was done before I got them to use modloader

GuiInGame.java renderGameOverlay(...)

//wave auto init
		if (mc.theWorld.zombieWave == 0) {
			//newWave = true;
			mc.theWorld.zombieWave++;
			mc.theWorld.zombieKills=0;
			mc.theWorld.waveSpawnCount = 0;
			mc.theWorld.waveSpawnMax=(mc.theWorld.zombieWave*3)+7;
		}


//kill counter trigger of new wave init
if (!(newWave) && (mc.theWorld.zombieKills>=mc.theWorld.waveSpawnMax) && mc.theWorld.zombieWave != 0)
		{
			waveDelay = System.currentTimeMillis();
			newWave = true;
			//fontrenderer.drawStringWithShadow("You can move on to the next wave now!", 2, 80, 0xE52626);
		}


//more....
if (newWave) {

			if(System.currentTimeMillis() - waveDelay >= 10000) {
				if (mc.theWorld.zombieKills >= mc.theWorld.waveSpawnMax)
				{
					mc.theWorld.zombieWave++;
					mc.theWorld.zombieKills=0;
					mc.theWorld.waveSpawnCount=0;
					mc.theWorld.waveSpawnMax=(mc.theWorld.zombieWave*3)+7;
					//mc.displayGuiScreen(null);
					//mc.func_6259_e();
					newWave = false;
				}
			}
		}


TileEntityMobSpawnerWave.java

added in updateEntity()


if (worldObj.waveSpawnCount < worldObj.waveSpawnMax && worldObj.zombieWave > 0)
{
	//the usual entity creation code plus...

	//if ent made
	worldObj.waveSpawnCount++;
}






somewhere the kill counter goes up, cant find it heh, suicided zombies causes it to go up so its probably a hook into setEntityDead or something