I made some alterations myself. My first task was changing some base facilities. Stores were way to small and prison limits made me bananas.
I increased those generously. Then I made one soldier my sniper. Gave him 150 firing accuracy. This helped me combat the mansions and manors.
The toughest was the terror missions. There was no getting around those. It was like the Aliens were freebasing plasma on every turn. That and the ships turrets sent in me into a tizzy.
Congrats on your completion. I finished it on.. "New Years eve". It was gratifying as catching the
was a bit challenging for me. This is needed in order to access Cydonia.