I have 103 mods installed for Skyrim, I use Nexus Mod Manager to install them. But at the same time I keep trying out different ones, seeing what they are like, and uninstalling them if they are not working properly, or not to my taste.

I've been getting quite a few CTDs as of late, and I feel that some of the mods I uninstalled may have left a few remnants of script or other unwanted things behind, which possibly might be causing the issue.

So, my question is: is there any method of 'cleaning up', without having to completely uninstall the game, delete all the mods, and then completely re-install everything from scratch? It took me a great deal of time to get Skyrim running the way I want it, and with all the various mods configured properly, and I'd hate to have to do it all again from scratch.

Thanks.

The golden rule of installing mods is make a manual save and keep it safe somewhere before you go testing out mods. Give them a good try and if you like them fine, if not remove and go back to the manual save you made earlier.

Adding mods and then removing them on the same save is simply asking for trouble. Its just the way it is as scripts are stored in your savegame permanently.

You can try cleaning up scripts in your savegame with Hadoram's Savegame Script Cleaner but it not 100% guaranteed.

I would say you've more or less learned the harsh lesson a lot of folks never learn. Trying to play Skyrim like it's Oblivion or Fallout simply doesn't work. You can't just pop mods in and out on a whim - because you'll get into exactly what you have now. A game riddled with CTDs and old orphaned information you can't even get rid of with save cleaning tools.

Those tools can only do so much, and if any of the mods you had modified vanilla or DLC information, you're stuck with those changes. Your best bet is to decide what mods you want to keep, and throw out any saves you've been using up to this point and start over. It svcks, but this is the only way to guarantee you're rid of the problems.

If you are going to upgrade a mod like Immersive College of Winterhold, is it s good practice to run the save game script cleaner? http://www.nexusmods.com/skyrim/mods/52363/?

Or can the script cleaner cause more harm than good? I've read various things, so I was wondering what your advice is about using the save game script cleaner.

Well, this would kind of be starting over, but one good method for handling mods, including trying and removing them if you don't like them, is the Mod Organizer. With this tool you can even create different profiles of mods for different users. Unlike usual mod installation, Mod Organizer creates a separate location and mechanism through which mods enter the game, without affecting your vanilla installation at all.

The STEP guide for Mod Organizer is here: http://wiki.step-project.com/Guide:Mod_Organizer

the Nexus location to download it here: http://www.nexusmods.com/skyrim/mods/1334/?

Beyond that, there is a good tool for cleaning installs & mods, called TES5Edit. Whether it would work with your set up or not I don't know. Here are some videos about using it:

By GamerPoet

https://www.youtube.com/watch?annotation_id=annotation_3835578397&feature=iv&src_vid=s3FZ4bMTWgQ&v=i50wxDuEnn0

By gopher:

https://www.youtube.com/watch?v=fw3g_N1jcZQ

https://www.youtube.com/watch?v=UOQO2S6HDBw

I found the above very helpful for helping me manage my mods and reduce CTDs. I still have a few mods I installed before switching to Mod Organizer, but most of my mods are done through this tool and it is very, very helpful.

This may not be of any use to you, unless you do decide to go back and start over reinstalling everything for a new run through. If you do decide to go back and clean up from the beginning, however, I would highly recommend going the MO route when you do. It saves a ton of headaches later on, and gives you a lot more flexibility in how you handle your mods.

The cleaner should be thought of as a tool of last resort to revive a save that's been damaged through bad practices. It works, but the results are not guaranteed and may not come out as you hope. Especially when dealing with vanilla game material. It's not something that should be handled with the same casual approach that we all use with TES5Edit.

That all depends on your definition of a headache. The virtual file system and the BSA management features have both been sources of headaches for popular mod authors even though most won't say so openly. MO is not something I ever recommend because those two features alone have resulted in so many silly support requests for my mods it's not even funny.

About a year ago, I tried hard to follow the precise directions to get a truly perfect MO install going. I got about 16 steps through the 30-some-odd steps sequence and realized the author was making all kinds of assumptions about my knowledge of the technology involved. My questions to the Nexus thread were never answered as far as I know.

So, if you have the knowledge to do an MO install and make it work more power to you.

But even I can install NMM and it works. Granted it doesn't have many of the features that I hear people talk about in MO, but given I cannot even get MO installed I wouldn't know for sure.

Well, I respect your perspective and knowledge as an experienced modder, Arthmoor. I am sure you know a lot more about all this stuff than I do.

However I can say I have not had any significant troubles with MO, and my game runs pretty well most of the time. With more than 68,000 endorsemants for MO on Nexus, a lot of others have also found it quite helpful. As a mod user, I have found it to be the best mod managing tool I have tried yet. Granted, it did take me a little time to learn how to use MO. But there is a fair amount of material in the STEP guide and related resources and videos for people to get things working well, if they want to take the time initially to set it up. I found it did help a lot to watch the tutorial videos as I went along, especially from Gopher and Gamerpoets.

But "different strokes for different folks" -- not everything will appeal to everyone.

Why didn't I make backups of my save file?

Well it's too late now, and the harsh lesson has been learned.

Having said that. I downloaded the script cleaner mentioned above, ran it, and deleted a whole bunch of 'orphans', and other things, as directed in the instructions, and since doing that I've not had a single CTD - so perhaps I've gotten away with it this time.