I just took another look, and I'm pretty sure it didn't place them there on purpose - I'm pretty sure your illusion mod is too new for BOSS to recognize it, plus it doesn't make much sense for them to be placed after tha bashed patch. Try placing them earlier in your load order next to similar mods according to the BOSS masterlist.
It shouldn't leave any stragglers, but I've seen earlier versions of NMM do just that - have a look in your data directory and have a look in the scripts folder, see if there's anything that shouldn't be there.
That should be more than enough considering your modlist.
Have you ever messed with your ini file? May be worth deleting and letting the game autoregenerate.
How random is your CTD? One thing that cleaning your mods won't do is repair navmeshes - with worldspace edits these can conflict quite easily - BOSS will notify you of these, but only if they've been reported to the BOSS team by other users...you could always load up TES5Edit and have a look and see if you notice any navmesh edits that could be causing problems.
If all else fails, try a binary troubleshoot - turn off half your mods, start a new game, and test. If it still CTDs, deactivate half again, and so on, until you find the culprit.