Lauren

The last CPU-related setting (fPostLoadUpdateTimeMS) will not affect your framerate, but will affect your load times. Unlike the other settings, Papyrus will use the entire time even if it has nothing to do. Increasing this will only help make sure cells and such are set up if there is a load screen. For example, the civil war can stress this because it has to set up a ton of things in the cities for the war when you enter through their load doors.
https://forums.bethsoft.com/topic/1487930-getting-a-lot-of-script-lag-going-over-10000-ms-sometimes/?p=23340131

I follow (mostly) SRLE myself and I also get the same warnings. People have brought it up before I believe in the main SR thread*, and Neo said to ignore it as everything has been tested as working fine. I've re-ordered them before, and currently they're not re-ordered as I'm redoing my setup, but I haven't actually really played the game so no effect to report either way.
 
Also, SRLE still uses BOSS. The PMOP is solved by moving the mods in the left pane around, it's not really the plugin (esp) load list? There are no special instructions for the BOSS ordering of most of those mods, as they've been around awhile and are on the BOSS masterlist.
 
*found it: OP - https://forum.step-project.com/topic/1209-skyrim-revisited-pre-release-feedback/page-241?do=findComment&comment=87368
TL;DR from Neo:
 

Just manually drop the folder into the mods folder (i.e. skyrimMod Organizermods or wherever yours is). Right-click in the left pane of MO and click Refresh. It should show up somewhere (the bottom of the list for me) and you can check to enable it.
 
You may need to alter the folder structure first as Aiyen describes above. When you open the folder that the archive unzipped to, you should see folders "meshes", "textures", etc. If it's not like that, make it so. (Aiyen's first sentence is referring to putting things directly into Skyrim's data directory, which of course circumvents the point of MO.)