As I've wrote before - I'd avoid merging any cell or worldspace records and stick to merging game tweaks and scripted actions. Make sure what you merge is white compared to each other in tes4edit with the filter on.
Right, thanks Psymon I will check that. So far I've only merged Companion Sound Sets, a bunch of dialog files for giving companions custom dialog. I've gotten a lot of info just from this thread though, some of it obvious, some of it not so.
The only way I could see merging providing a performance/stability improvement vs leaving them all separate is if you were approaching the limit on the number of files the Data folder can have in it before the game goes loopy. This is generally anywhere between 350 and 400 file. Almost a certainty above 400. Files being any ESM, ESP, *AND* BSA files sitting in Data, whether they be activated or not. Merging reduces this number obviously, assuming you're getting rid of the original data files when you do it.
Okay cool. I have been keeping my data folder clean, so 95% of my mods in there are actually being used, the rest are ghosted. If I have ghosted mods, is there no theoretical limit to how many I can have in there? It might just be my paranoia but I've been keeping even the ghosted file count down.
If you're far enough under the count limit I can't see it helping since you still have the same amount of actual game data regardless.
Rats! I'll post my interior cell bug in a new thread, maybe I can get some insight. However I've done quite a bit of testing and doesn't appear related to a particular mod.