I use an extensive amount of mods, and I've been having this issue where certain NPCs who are supposed to give you Miscellaneous quests simply aren't giving me the option at all. The events I know specifically are:

Ysolde won't give me her favor quest (Where you collect mammoth tusks).

Most innkeepers no longer have an option for "looking for work"

Uthgerd the Unbroken will not give me an option to brawl with her.

Carlotta Valentia won't give me the dialogue option to convince Mikael to leave her alone.

I can't quite figure out what mod could be doing this, it's happened across multiple different characters and I can't seem to find the culprit doing it. Here's my load order:

Most of these mods are Companions, Houses, New Items, AI Overhauls, or new Enemies/Wildlife. I don't have anything with the exception of EFF that implicitly states it affects dialogue options. This is a relatively NEW issue and while I've tried the game with my newer mods disabled I still have this issue. The only other thing I've done differently lately is I finally cleaned mods suggested by BOSS to be cleaned, I checked the mod descriptions for each one I cleaned first and ONLY cleaned the ones that did not rely on dirty edits, the only changes I did through TES5Edit were Remove Identical to Master Records, and Undelete and Disable References in the mods suggested. I also have began using a Bashed patch to combine level lists together.

So does anyone have any suggestions for how I can find out which mod is the culprit for this? I eliminated most of the mods that I think could potentially do this but can't figure out why it's still occurring.

You have quite a few NPC mods most are companions.

Most of those mods I have not heard of.

The Bounty Gold mod might remove the option for getting bounty quests from taverns. I am not familiar with that mod.

It happens actually because your saves relying on those mod's, so if some mod's are the culprit of that situation (not giving NPC's favor quest), disabling that mode will you gain nothing.

I thing your saves code are altered because of those problematic mod's !!!!!

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But it can be something else (glitch - strange main quest behavior):

For example: Ysolda's Mammoth Tusk quest is one of several "fetch" Radiant Quests. If you have another fetch radiant quest started, then you'll have to complete it before you can start Ysolda's.

If you joined the Companions and brawled with Nazeem, the option to brawl Uthgerd will disappear.

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...but it is possible that you have a mod that alters quest givers in any way, or affect NPC's A.I.

I use lots of companions since I like to add them to my home base to make it more "lively", also I beef up the Skyrim difficulty with other mods to make it more party-reliant. I probably don't need ALL of those companions (some are very bland) but I don't see how they really would have affected dialogue trees with non-companion NPCs.

Bounty Gold allows you to use MCM to adjust the amount of gold rewarded from bounty style quests, I will try to run with it disabled and see if I get bounty quest options from innkeepers again.

I was aware of the Radiant Fetch Quest issue and I don't believe i have any other fetch quests initiated (at least not according to my quest log). I'm not a member of the companions nor have I brawled with anyone else (though the drunk in Riften still offers to fight me) so I don't know what's up with Uthgerd.

I will try a new game to see if I still have these issues or if save game bloat was causing issues.

Most of the mods I have that impact quests I have disabled, they were Better Timing that lets you adjust the level you receive quests (which shouldn't affect favor quests anyway), and Better Quest Objectives which should only affect quest descriptions and book text. I have a few dialogue mods that are simply UI based (Better Dialogue & MessageBox Controls) that shouldn't impact the actual NPC.

I did recently switch over from UFO to EFF for my follower mod (I'm having issues with the Viconia mod where she will NOT give me the dialogue option for her to join me, I still can't fix it but I thought UFO might have been the issue, still I like EFF better) but I don't think EFF should impact any NPCs that are not followers.

Currently the issues aren't severe, other than not being able to recruit Uthgerd I don't particularly care but I'm not sure to what extent this damage may have been done to other NPCs.

It may be that your Story Manager is stuck. See here: http://www.gamesas.com/topic/1447502-sendstoryeventandwait-not-returning-either-true-or-false-what-can-it-mean/

On my LTGJ mod page http://www.nexusmods.com/skyrim/mods/14509/? see the sticky post on how to enable logging for the SM.

If that's the case and you see those timeouts please share your log on pastebin or somewhere and you can try my fix also located on LTGJ download page. Carefully read that fix instruction if you gonna use it and know the issue will reappear.