For the groups related only to the borg wall shields, what you want to do is go through each spawn after each transformer and kill everything BUT the MED. Drone. the others are to die, only when you have 4 medical drones, 1 from each transformer spawn, you do the final full transformer activation.. in doing it this way you WILL NOT have any spawns except worker drones.. and there then are only 2 things you need to worry about
a) the workers
b) avoiding the medical drone from pumping you full of nanoprobes