For some reason my world starts with a tier 3 factory already built and placed, if i pick it up it makes it so that i can no longer use the combinator

Have you managed to leave the factory somehow? Or did you spawn outside of the factory itself? The game should start with a tier 3 factory placed and you being inside of it, though I have no idea how you left it.

I was launching the scenario and for some reason i would spawn into a tier 3, with another tier 3 inside of it. This was all with the world gen settings as well. After a while i just launched a freeplay game with the game settings and it seemed to work. not sure what was going on with the scenario though.

What mod version are you running on? Try updating to the latest, as I don't have any scenarios - only different world gen settings to keep the biters away.

I was running 1.2 I'm not sure why but i had it in my mind that the mod was a scenario. Been playing for about 13 hours now and loving the mod

Nice. Seems that it's more people thinking that this mod is a scenario, so I'll put that into the readme. Have fun!