I was playing FO:R since late season 2 up until early weeks of S3. Now , I always was noob and got killed a lot of the times, scavenging, locker-hunting, caving or just exploring.
Yes, that's fine. The game is about killing, dying and reading, sometimes writing.
To give you context on ~40 lvl Gun Runners mutant quest was still challenging, although it was noticeably harder to die because I got implants.
Sorry but I have to ask you: are you trolling? The Gun Runners mutant's hideout quest isn't challenging and hard. It's great quest because even loner can kill those mutants and get cool reward. This quest is doable both in turn based and real time combat but for the second it's highly recommended to do it with more people. If you're alone then take TB combat, use good gear, use cover, think (!) and you will do it.
...wearing CA+ Combat shotgun and I wasn't able to kill her in TB(Brought her to around 100 hp twice).
Combat shotgun is low tier weapon and you should use better weapons as soon as possible. Also if you use CS, don't forget about getting green ammo which does more damage. You can buy or craft ammo, it isn't hard to get it, believe me.
I've already lost all my in game friends because they weren't able to find their way through S3 meanders.
That's sad but you could find others friends. You should join player faction or find random people in most common places such as Hub, forums or discord chat.
I know that most of you will be like "its not game for you scrub"...
Nope because the game is for everyone who likes Fallout and FOnline. Season 3 is very "noobs friendly" because you don't lose your gear, there're a lot of quests and PvE activities. However keep in mind that you need proper build and from time to time think what you do. Cheer up and don't worry.