This issue happens a lot. the Enderal system runs unusual scripts in the background. i believe the CTD is a result of vanilla skyrim runs on a default 32-bit program format.
installing mods that reduce some things like optimized textures and LOD's helped with frames-per-second and the loading times but it did nothing for the CTD's happening randomly in a zone or a load screen.
I am sorry this does not help your issue but i personally recommend changing your autosave settings to be more frequent.
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I am using a intel i5, GTX 970 dual SLI, 8GB ram, 500GB SSD HDD. fps rapidly drops around waterfalls and small streams due to its compressed textures but the game runs good for the most part.