Don't worry, Junktown is unimportant. My character eliminated almost whole junktown too. After the assassin with the shotgun shot at Killian, Killian shot back and accidentally hit Ian. Ian didn't like it and shot back. After the assassin was killed Killian's men were still shooting at Ian and I had to help my loyal companion fighting those idiots.
Didn't matter much that I killed almost the whole town (didn't they learn from Killian's death to leave us alone ? ), since I killed both the good and the evil guys not even karma suffered, besides the loot and XP I was also rewarded with berserker reputation and a very nice picture.
If you want the dog to join you wear leather like its previous owner or feed it. If it joins it will stay with your character until it dies or the game is over (it's very hard to keep it alive later in the game), you can't leave it behind temporarily.
It's possible to get the quest item for the brotherhood without Rad X if you just run in to get it and run out afterwards, but if you travel so far you want to take your time exploring. You'll need a rope to enter, it's the last location where you need one. You'll need to take 2 Rad-X for 100 percent radiation resistance, partial protection isn't enough. Don't waste time with reading books, using healing skills or doing other things which let hours pass, Rad-X lasts very long, but not forever.
Companions never get radiated or poisoned, just imagine they are mutated or have their own dose of Rad-X. Take Ian with you, you need carrying capacity for the loot you'll find.
You can buy Rad-X from Vance, the chem dealer in the eastern Hub, in the northeast of old town. Jacob or Lemmy can give you a recommendation or you can try directly pressing the barter button or killing him if you can't convince him to sell stuff to you.
The Glow is the only location where Rad-X is needed, so if you've already found 2 in the Necropolis vault there's no need to buy more.