I'm new to modding Skyrim, but I could look. Best thing you can do for yourself is carefully read the requirements of each mod to ensure you a) have all the required files, and b) put them in the correct load order.
Downloading LOOT (Load Order Organization Tool) does a lot to help with that, but can't get everything right, so make sure to check the order after you apply the LOOT changes to make sure any files necessary for certain effects (for instance, Amazing Follower Tweaks should be placed after (lower than) any standalone followers, or mods adding followers to the world, not because it provides conflict, but because any follower that loads after AFT will not be affected by it).
It couldn't hurt to make sure you have TES5Edit, which helps clean up file scripts, I believe, which some mods need, or could very greatly benefit from (such as the unofficial patches).
I have no idea if you've tried it all and it just hasn't worked, or if you ddidn't know about LOOT and TESEdit, but I've had to resolve some mod conflicts recently, and these took care of everything. Except the crafting overhaul -- I'm still not sure what it was about the weapons and armor fix that was causing a CTD, but I intend to find out.
Lastly, if all else fails, you just have to disable everything up to the last stable configuration and do the things that cause CTD's (or whatever other issues you're seeing), to identify the specific culprit.
That's the extent of my knowledge on the subject to date. I hope it clears up the issue, though.