I think I remember reading on here that there is a way to look at which mods are conflicting or causing problems using TES4edit? Where you can load up the Load order in the program and look for errors within. I'd love to learn how to do this and it sounds like an amazing way to iron out the last few bugs in my LO that are still causing CTDs. I'm an avid user of BOSS, but I don't think it shows all potential conflicts in an LO. Thanks for reading everybody. and for your help.

Yes, with TES4EDIT you'll be able to see most conflicts.
But some conflicts are more subtle and will not be detected, like two mods changing the layout of an interior cell or different scripts that modify the same records, for example.

Also keep in mind that just because TES4Edit says it's a conflict doesn't mean it's something to panic over. Two mods moving the same rock to different positions, for example, shows up as a conflict but obviously isn't important.

Make sure you're using an updated version too, Elminster has been making updates recently which fix a few annoyances and bugs.

Awesome, thanks. Is there a guide on how to check for conflicts with TES4Edit?

I would be interested in that too. My mod list is finally complete and I`m checking now everything for incompatibilities, so get used to TES4Edit and Wrye Bash is absolutely necessary.

Note that TES4Edit has no idea about logical script conflicts though. So if you try installing both Living Economy and my Enhanced Economy, TES4Edit (and any other mod tool) will detect absolutely no conflict, but the two are completely incompatible due to their scripts.

Go to the Nexus FO3 downloads, search for FO3Edit.

I thought I could combine most if not all of Duke Patrick's mods but I don't think you can with the scripts or something. Correct me if I am wrong but it seems like merging then causes conflicts internally.

I think BOSS points out many of these sort of general script conflicts doesn't it? I'm referring to the more specifically detailed conflicts that Boss doesn't have the power to detect.

and F03edit? as in Fallout 3 edit? does this work for oblivion in the way we're discussing?

TES4Edit/FO3Edit/NVEdit are all the same program and only changes function based on the name of the EXE file. The FO3Edit topic in the Fallout mod forum has a really good HTML guide to the program in there somewhere. Or you should be able to find it on fo3nexus.com.

Probably only a small fraction.

BOSS doesn't have the power to detect anything by itself. All the conflict info you get from BOSS is text manually added by people reporting the errors.

The reality is you kinda have to get to know how mods work under the hood if you want to be able to 'predict' conflicts. There is no sure fire way of detecting all conflicts other than to understand how the mods in question work and making educated guesses.
TES4Edit will detect tangible conflicts, IE, formID's that are overrided.

For the intangibles, such as what Petrus and TheNiceOne were mentioning. You will need experience, and/or advice, and/or get your hands dirty with the CS.