Ringing the gong will reset your quest log, so any remaining entries will be cleared when you move to the next and final area (one way trip).
For the Marcus / Tingalf quest, did you join the merchant's guild and ask the head of it if there was anything you could do for them? He gives you part of the quest (if you have already had Tingalf arrested, you should just be able to say so to complete that part of the quest).
If you already did that, I wouldn't worry about the quest entry. That quest is fairly involved, and seems to be easy to partially break by doing things in too unexpected an order.
After talking to general Alix, did you enter the castle before talking to Mitox, or did you do that right away? If you entered the castle first, that could be the problem. If not, I'm not sure what it is (don't recall if you actually get a sealed letter in your inventory or not). In any case, the experience you would get from poisoning the well and blowing up the suply train are not enough to worry too much about missing.
The cult followers react to your talking to the statue, rather than opening the gate. As long as you have the correct book in your inventory, the statue should speak to you, though you only get one chance to answer its questions. Had you spoken to it and answered the questions correctly, you would have gotten a level of Restoration as a reward. You could use
iZakaroN's SaveEditor (or from
Kiya's site, with description) to give yourself a spare skill point to add to Restoration, to make up for the game 'cheating' you out of that reward. Using Lockpick to get in should not cause any problems.
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