Wow, you are playing with a lot of options turned on. That makes the game much crazier. Sounds like Hybrids+Advanced Hybrids, Dyson Sphere and Botnet Medium at least.
Just some comments on the Botnet and such:
Botnet does a TON of damage. So much, that you can often leave it under a Force Field and it will still kill anything it attacks despite having reduced damage for being under a Force Field. This helps keep the Botnet alive. In particular, this tactic is very strong when you are using the Botnet to protect the planet a wave is hitting.
On the Golems, Spirecraft and Botnet settings: These each have 3 settings, Easy, Medium and Hard.
EASY
This just gives you new toys and no disadvantage. It is an excellent way to learn each of the settings. You still need to find the toys to use them. Golems and Botnet (which is a type of golem) just need to be repaired as you've seen. Spirecraft are built from Asteroids that appear randomly in systems (but only when you have them turned on, so if you don't yet, you won't have seen any of the asteroids).
MEDIUM
For Golems and the Botnet, these trigger an AIP increase when you repair them, and they cost a lot more Energy than on other settings. Spirecraft are a little different on this setting: They can't be repaired...ever. Since there are a limited number of asteroids in a game, your supply of Spirecraft is limited.
HARD
This is like the easy setting, but the AI gets to send a big nasty wave called an Exo Wave (for Exo-galactic meaning "from outside the galaxy") that can have some extremely big and nasty ships. If you turn all three (Golems, Botnet and Spirecraft) on Hard, the AI gets to send THREE Exo Waves! This will hurt a lot.
So, when selecting what you want to play with, try and avoid HARD until you've gotten more experience in the game because you really want a handle on everything else before you start dealing with Exo Waves. Both EASY and MEDIUM are good choices for learning about each of these factions.