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In Old Ebonheart quests the Thieves Guild and Fighters Guild are at opposite extremes for faction reputation: the TG questline is much longer than all others but it rewards less faction reputation, I think the positive amounts should be increased in some of its quests. TR_m3_TG_Moranie3 could give +10 instead of 5
The OE MG quest Don't Touch My Gems! is a misc quest and not a faction quest, but it should remove MG reputation if the player gets the questgiver killed (only if the player is a member until this has been implemented).
Morag tong: Older quests like this one could also add effects on faction reputation (only if the player is a member for the same reason)
The OE TG betrayal option "They're all dead? Here's your 10,000 septims. Now get the hell out of my sight. I don't like traitors. Even ones that are working for me."
has no negative reputation in a questline that's generous with negatives :P
EEC issue: TR isn't supposed to promote the player to the last ranks like the Raven Rock questline does. TR dialogue in the "promotion" topic technically allows it if the player gets enough faction reputation. You probably still can't get to 100 reputation with current quests so it's not a concern but you might in the future. Copied refusal responses from when TR was using a duplicate faction or in the old faction merging mod: