That just means you need to rebuild your Smash Patch as you have changed your load order. Though having the ESM/Ps out of order doesn't matter to the Smash Patch, so the game will be fine, however you had them in a different order when you last built the Smash Patch, so there may be other changes you have made which require resmashing. EDIT And, delete the SKSE plugin for Audio Overhaul Skyrim, you don't need it.
I had the exact same problem, eventually found her crouching (so hard to spot with the grass around) by some rocks off the road. If you've installed the entire guide, then you'll have the "Instinct" option from the wheelmenu - use that to add a temporary shader over her, should help.
For your problem 1) this was caused by a 3DNPC banter patch which came with the mod Song of the Green (Auri Follower). The patch had some accidental edits, one of which prevented Daenlyn from spawning in-game. The author of Song of the Green has removed this patch for now due to lack of available time to fix. I suggest that if you are planning to take a break anyway, that you wait until Legacy of the Dragonborn v5 has been released and this guide updated to use v5, then reinstall the guide from scratch and start afresh.
Or you could find out which mod is the problem and reinstall it. Simply exclude some ESM/Ps from the Bash patch by unticking them. Rebuild the patch, and if the error doesn't reappear then the problem mod is one which you unticked. Narrow it down to one single ESM/P file and that's the problem mod.
I was mildly curious about that too. It would be a great help if when removing an INI edit or special instruction, the changelog stated exactly what had been removed and/or what default to revert back to.
Hoth is only meant to use his custom equipment. I believe the author says somewhere that trying to give him other gear causes Hoth to appear naked. Personally I found Hoth rather dull, he only has around 3 idle comments which he repeats over and over, and he never offered any bounty quests at all, so I dropped him.
Yes I remember you couldn't reproduce the problem when it first appeared, I can only assume that there is some difference in how zEdit is setup/installed or about MO2 - it could be as simple as you having extracted updates to zEdit on top of older versions which had a file no longer included in zEdit, and that file negates the problem for you, but those of us who didn't have a zEdit install that old (or deleted and replaced the zEdit folder with an update) lack that file. That's just an example of a possible reason. Another possibility is that you and your team have edited one or more of the affected ESP files at some point in the past and forgotten, and that edit is the reason you don't have problems now. Or some config file from the game or from zEdit or from MO2 etc. is forcing zEdit to read your masters in the correct order, but is not for other people. Many possible reasons.
That's because zEdit messes up the load order for the masters. Instead of loading the masters in order as the game reads it, zEdit (zMerge) loads the masters only as each new entry in the order requires them. You can see my earlier post identifying the problem here. Updating YAWTO Aspens.esp masters list is the workaround if using the clobber method (which is the method the guide says to use). So if the improved method doesn't have this issue, then the zEdit author must have fixed it for the improved method but not the old method - in which case all merges should be using the improved method instead. It is afterall, apparently "improved" which is something of a promotion for the new method in itself.
I see, and is there a reason why you choose the old clobber method? I use the old method only because the guide says to, assuming there must be a reason. So is it actually failing? Or is it ultimately succeeding with various warnings about missing meshes which it then skipped all references to? Manually extracting the archive into the correct mods folder should resolve it, if MO2 is somehow failing to extract all the files.