Try playing without the mod enabled to see if it's actually FSQ that's causing it. If it is the issue, then I don't know why or how it'd be doing that.
I have the same issue, shame because this is the only sidequest that i wanted to repeat to get a Fibber for Gaige :D "!" icon is above Mal, but can talk to him, tried without any mods and its the same, so maybe because of that? When you finish his quests, you cant interact with him anymore? Most other NPCs have a interact/talk prompt, he doesnt.
Small nitpick to your description: One of the best SMGs (the Sandhawk to be precise) is the reward for one of the main quests in the pirate DLC. Another weapon in that DLC is the "Thief" pistol, though I think (haven't tried it yet) that the relevant mission is repeatable so you can farm the rakk-hive and the leviathan.
By the way, how are you able to redo that mission (Where do you go to get it again)? Or, if you just looked through the code (or either way), can you tell me which mission internally needs to be removed?
If you could provide screenshots, that would be great.
It will be neat to try out this mod. The only problem I have is with the Sand Hawk, the final missing puzzle piece for (all) my Maya build(s) isn't farmable. As if the Captain Scarlet DLC couldn't get any better, one of the best and most useful weapons in the game that it introduced, is achieved from a one-time main quest. *sigh*
I recall that the Sandhawk is farmable with the Community patch installed. It can be obtained by farming the guy from the "Just desserts for desert desserters" sidequest. At least, I think so.
That's a side effect of my decision to leave Story Quests out of the mod. Additionally, the SandHawk is among the strongest weapons in the game. Especially considering UCP mentioned above, it's not really "balanced" to make that farmable from its own quest.
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One of the best SMGs (the Sandhawk to be precise) is the reward for one of the main quests in the pirate DLC.
Another weapon in that DLC is the "Thief" pistol, though I think (haven't tried it yet) that the relevant mission is repeatable so you can farm the rakk-hive and the leviathan.
If you could provide screenshots, that would be great.