So when given the option to build the structure with a faction I selected the Minute-men, when I used the structure I failed the first mission with the Railroad because I didn't alert them about something relating to the courser chip and so on. So I reloaded because I wanted to not fail that quest. So I've done a few things with the Railroad again and I'm ready to continue with The Molecular Level and use the teleporter again, only problem is when I loaded the game after failing the first Railroad quest I loaded after choosing which faction to build it with so I can't side with the Railroad like I now want to. So will this affect my progress with the Railroad, can a still complete their quest line after building the teleporter with the Minutemen?

You're fine.