This probably isn't an issue, but your enblocal has two [Window] subsections, one turning off and the other turning on fullscreen borderless. Also the reserved memory in it is rather low at 128mb, have you tried increasing it to 256/512? In the first post you say you were using 512 but your enblocal says differently, so I am just seeking clarification. Also follow kabepo's suggestion and make sure this isn't an issue with vanilla skyrim.
Skyrim has never liked my pc either, so after suffering stuttering like you for multiple years I switched to SSE 2-3 months ago and haven't looked back, imho more stable (framerate and ctd wise) than skyrim ever was.
Skip my entire first post as, I reread the original post and found that you had already done this. The second part of my first post is still applicable. Sorry I wasn't able to help.