I am using STEP v2.2.8 as my bible, and using Mod Organizer (MO) as my mod manager. The list of mods is http://wiki.step-project.com/STEP:2.2.8#STEP_2
I have a pretty solid machine - i7, GTX 480 (may seem dated to you, but is more than adequate for running vanilla skyrim at Ultra).
I was playing modded Skyrim (using STEP v 2.2.8 Core + some other mods) just fine when on a regular HDD. Decided to free up some space on my SSD (removed modded Oblivion), and move over Skyrim there to take advantage of SSD loading times. Used the Steam mover application to move over Skyrim files, which worked fine but BOSS did not recognize the Skyrim location and threw a fit. Modded game was still running fine.
Decided to reinstall Skyrim (from scratch) on the SSD via Steam. Vanilla Skyrim works fine. So now trying to recreate the modded STEP Core system again on the SSD. Moved the Mod Organizer mods folder to SSD to take advantage of SSD again.
I install a few mods and test if Skyrim runs, but am getting very inconsistent CTDs on loading now. This is a clean install, and the way MO works, it does not touch your vanilla files anyway.
I installed all mods until "http://www.nexusmods.com/skyrim/mods/9080". now the problems begin - game crashes before the main menu. Remove it, it now crashes again. Add another mod, it will load, try again, it will crash again. Same thing with "SMIM", Skyfalls+Skymills". There is no consistent pattern, adding a mod X - game loads, adding another mod Y, game crashes. Removing mod Y and reverting to previous step, game crashes! Try again, it may load to main menu and game is fine. But this is not always consistent - it may work fine at other times. Crashes always happen on load - it either goes to main menu, or crashes on creating the SKSE windows.
SKSE v 1.6.16 (last stable version), also using Sheson's tweak through SSME. SKSE creates a game dump on Skyrim crash, but not sure how to read it. Any pointers on why this may be crashing? I may be new to Skyrim modding, but am an experienced mod user for Oblivion. What is baffling is the inconsistency - a repeatable crash leads to pointers for a cause, but this is just frustratingly random now. Help appreciated!