One of our Spartans (loyal member of the SoT community) by the name of CrushBoss, is an optimization guru and has wrote several guides to aid new (as well as old) Skyrim players in modding their game.

He has compiled the following guide to "clean-save" your game as thoroughly as possible by utilizing new tools that can help with this process.

(Before doing anything to your save game BACKUP your save file. Otherwise it may end up in Oblivion.)

Proper Clean Save Procedure (by CrushBoss):

The purpose of a clean save is too remove remnants of older mod versions or removed mods. Keep in mind that there is no such thing as a true clean save. Some remnants of the old mod/s is usually left behind and can later bite you in the butt. I usually backup my entire Skyrim and Save folder before doing so. This makes it easy to revert back if things go south later on. I only share this procedure to help give others the best chance of success when doing a clean save.

Before making changes load your Skyrim game and do the following:

1. Go to a location that will be unaffected by any and all mods that will be removed or updated (whenever possible). Most player homes are good for this purpose. Always save in a small interior space with little going on. For example if you are uninstalling a follower mod you wouldn’t want the follower in the room with you (common sense) or if you are uninstalling an armor mod you wouldn’t want to be wearing the armor.

2. Some mods with MCM support have a Clean and/or Disable or Deactivate setting/feature. A few even have an Uninstall feature in the MCM menu for the mod. Use the Clean feature (if applicable) and then Disable, Deactivate, or Uninstall the mod (if applicable) in the MCM options.

3. Sleep for seven days to make sure all active effects wear off, scripts finish processing or timeout, and most active threads close. I recommend using the ‘No Boring Sleep-Wait Menu’ mod for this purpose.

4. Open up the console and type ‘pcb’ to purge the cell buffers.

5. Create a new save and then exit the game.

6. Uninstall the mods you no longer wish to use or that you are upgrading. Follow any special uninstall instructions for the mod. The mod's website or readme are a good place to check. Also make sure you uninstall or deactivate (in the case of a mod upgrade) any addons or compatibility patches that were installed with or for the removed mod/s.

7. Run BOSS* or LOOT* to re-sort your load order. If you are using a bashed patch (created using Wrye Bash) then re-build your bashed patch also.

8. Launch Skyrim using the save game you created earlier and ignore all missing mod warnings. Sleep another seven days and create a new save. Exit the game. If this step causes you to CTD try again. If you CTD a second time then skip this step and move to step 9.

9. Download, Extract, and Run ‘Savegame script scalpel - Papyrus Data Transfer’ - PDTWrapper.exe. It will select your latest save game by default. Click on ‘Load Papyrus Data Section’ and wait for it to finish. Follow the instructions under the ‘Analysis’ tab. In most cases you will be told to run ‘Remove Unattached Instances’ and then ‘Remove Instances’ selecting ‘Remove instances with undefined classes only’. This will fix most of the old script instances, references, and pointers in your save game.

10. Launch Skyrim and load the edited save game. Don’t click ‘Continue’ – instead click on ‘Load’ and make sure the edited save is the one being loaded.

11. Wait for two minutes (doing nothing) and create a new save. Exit the game.

12. You are now ready to install any mod updates or add additional mods. Install them.
(Note from GhostAgent: You obviously skip this step if you are just uninstalling/removing a mod.)

13. Run BOSS* or LOOT* to re-sort your load order. If you are using a bashed patch (created using Wrye Bash) then re-build your bashed patch also.

14. Launch Skyrim and load your latest save (‘Continue’). Wait for two minutes and then save your game.

15. Enable logging in your Skyrim.ini file and closely monitor your Papyrus logs for errors or problems. Papyrus0.log will always be the latest log file. Re-run steps 9 and 10 if needed (shouldn’t have to in most cases).

[Papyrus]
bEnableLogging=1
bEnableTrace=1
bLoadDebugInformation=1

16. Play and enjoy the game!

*BOSS and LOOT are third party applications that the modding community have written to aid in properly ordering your mod order--of course both are completely free.