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https://en.uesp.net/wiki/Morrowind:Factions#Reaction_Table
That is why it is a bad idea to join factions who hate each other like Mages Guild and Telvanni House simultaneously. And a good idea to join factions who like each other like Fighters Guild and Imperial Legion.
So usually it's not the perfect idea to join every single faction. But that's more or less still possible except mutually exclusive factions like Great Houses.
So if I wanted to join the Mages & Fighters Guild, that would be 2 Guilds so as not to get into a tricky situation to maintain a reputation?
Like, for example, the code book quest for the fighter guild.
But Thermal Lance is totally right too. Quest of a faction can (and will) break a questline of some other faction. So, OP, don't hope that you can complete 100% of quests of every single faction.
It's worth mentioning too that it's possible to become head of both the Fighters & Thieves Guild 'without' having to resort to the 'Code Book loophole' and worry about future complications; it just requires doing some additional quests to make up the reputation in either faction (Bal Molagmer for Thieves, Lorbumal's quests in Vivec Fighters Guild).
Outside of the Fighters/Thieves guild conflict, the option to only select 1 Great House, and the 'Temple hating the Nerevarine' for part of the Main Quest, faction conflicts are basically inconsequential in Morrowind once you've advanced enough in a particular faction.
Yes, these two quest lines are in contention, and you'll have to choose a side.
If you side with Sjoring (Vivec Fighters Guild, current guild master), then it's impossible to become head of the Thieves Guild.
If you side with Percius (Ald'ruhn Fighters Guild, old guild master), then part of your final duties will be to take out several of Sjoring's supporters. If this involves killing various people that are components of the final Thieves Guild quests (namely, Eidys Fire Eye), then you'll need additional reputation to advance within the "Thieves Guild" thereafter, which can be accomplished by doing some Bal Molagmer quests for Jim Stacey.
You will also need to be Guardian rank in the Fighters Guild (3rd highest rank, 70 skill), in order to receive the final quests to take out Sjoring's supporters. If you have not chosen to do the 'Code Book loophole', then you'll need additional reputation within the "Fighters Guild" to reach this rank, which can be accomplished by doing some of Lorbumal's quests in Vivec.