Restoring backup files from Time Machine without system preference/Library files

Well what happened was my laptop ran into 2 kernel panics within 2 days (I posted a question here: https://discussions.apple.com/thread/6132368?answerId=25605663022#25605663022). Which sent ME into a panic. I couldn't trust myself to go any further so I went to the Apple store who then helped did an erase/install for me because they suspect it could be a software issue (maybe it was missing codes or something) and suggested that it would be best for me to drag/drop restore my stuff manually. I'm not very keen on a full system restore either because I know there are some system files which I'd rather not have sticking around (like com.rims which are super stubborn to get rid of) and which could even have been the source of my trouble right now.

I was reading through every single page of Pondini's articles and I'm couldn't find anything which said I could just restore the apps in my apps folder without transferring anything else (ie. the library folder in the macintosh hd folder) since i'm assuming anything from the library folder of the user would be obsolete if I choose not to restore those files using setup assistant. But I'm more reluctant about not using setup assistant for restoring my apps because I don't know how bad it will turn out. Not to mention I won't know if they would restore system root files that should've been long gone since I uninstalled them.

Most of the settings which concern me are related to the Firefox browser (eg. bookmarks, saved passwords, scripts, add-ons etc) and apps like Stickies which I keep reminder notes etc.

So what you're saying is, I can just go ahead without restoring anything through setup assistant and do it manually using the Finder and drag/drop? And for any apps which I want to bring back its settings I look for its data(?) in the user Library folder? Would they ALL be in the User library/Application support folder? Would there be files I should be looking for in there? What about Parallels? Do I do the same with that? Or should I forget about that and just reinstall it? To what extent would I be messing up with Photoshop CS6 (any Adobe software for that matter) and Microsoft Apps when I drag and drop? What about third-party software that aren't downloaded from the AppStore?

(as for the issue of cloning, thank you for the suggestion. I will consider that in the future but at present I just REALLY want to focus on getting my MBP back up and running again.)

Ahhh that would be such trouble considering I accidentally left my Microsoft installation disc at home before going back to school. Is there really no other way to go about it for that? I guess I could ask Apple or Microsoft if they could provide me with a digital installation file instead for that. I would also actually just go straight and download Firefox and Chrome off the net and all but I mainly just want to make sure that I can access the old settings and the info I had saved on it.

I guess in terms of extensions like Flux and the Wacom driver I can easily locate and install again but there are some things like a fan moderator (which I use to keep the fan moving properly) and a ntfs-3g to support some mac incompatible external drives which I can't even remember the names of will be trouble...

So what I have to do now would be to just skip the setup assistant of restoring files from Time Machine completely then?

I'm so sorry for waffling on and on about the same issue. It's been really stressful and I really just want to get it right all at once and not have to think about it for a while.

I actually managed to remove the Blackberry software (I think?) before the second kernel panic happened but I wasn't given an explanation of the WD being the possible problem. I was told it would be better to start fresh so that I can scratch out the possible issues. Thing is, I don't know what the WD could've been doing because it's always been functioning like normal and it's a driver that connects to my external drive which is Mac compatible. In any case, I caved and went ahead of setup assistant and didn't restore anything through Time Machine. I'm going to try installing and restoring everything manually and hope for the best. But please do keep the replies coming as I really want to know for future reference if restoring JUST the applications from Time Machine would restore any redundant top-level library system files.

Re: because I was told that it would be pointless to fully restore something when it would also restore system files that were causing the problem in the first place.

This is the part where I get very confused. I've read on the community that it can be either hardware or software. But it's very contradicting on which is the cause as when I was at the Apple Store they said kernel panics usually happen from software issues where the computer is unable to read certain codes etc. They even ran diagnostics tests on my hardware and confirmed that everything is clear on that area.

What I don't really understand is why the kernel panic would occur with my external drive especially when everything is still properly installed etc. In fact, it was working fine for hours before the panic happened. Just throwing this out there in case it might be the actual problem: I had been running my MBP like a horse those two days with over 70-100 tabs open on several windows so that could possibly it? The genius who was helping me said it MIGHT have been pushing the ram too far and so caused the panic.

Regarding the first bit, I think that's what they meant when they said software issue? As in it being an issue of third-party software apps.

As for the RAM issue, I was throwing out a lot of possibilities for them but I think he refuted that in the end because the diagnostics didn't show anything wrong with it. But the nice thing was they at least said to keep an eye out for any trouble or future panics and bring it back in or something. I think the whole purpose of the erase/install was to root out or at least eliminate the possible system files (caused from unproper uninstallation etc) by dragging/dropping files/apps I want... It's an obnoxious amount of work if you ask me. I even asked if some of the dated software (Twitter, OSX10.6.8, Parallels, Video converter etc) might've been caused it but that was ruled out as well because they weren't running when the panic happened.

Regarding the first bit, I think that's what they meant when they said software issue? As in it being an issue of third-party software apps.

As for the RAM issue, I was throwing out a lot of possibilities for them but I think he refuted that in the end because the diagnostics didn't show anything wrong with it. But the nice thing was they at least said to keep an eye out for any trouble or future panics and bring it back in or something. I think the whole purpose of the erase/install was to root out or at least eliminate the possible system files (caused from unproper uninstallation etc) by dragging/dropping files/apps I want... It's an obnoxious amount of work if you ask me. I even asked if some of the dated software (Twitter, OSX10.6.8, Parallels, Video converter etc) might've been caused it but that was ruled out as well because they weren't running when the panic happened.