Main quest - I'd already explored Fingerbowl Cave long before and found the note, didn't know what it was for so I just kept it and went off. The quest update for the first seal popped up while I was far away doing some other quest, not certain what triggers it but it's definitely not intended right? Perhaps have the note only appear when the quest is actually started will be better.
I'll do that, you're definitely not supposed to be able to find that before the quest points you there. This is not the case with the Pillars of Wisdom quest however, you don't need to find the quest first before you can activate the pillars. In fact, the only thing that tiny quest is for is to make you aware of the existence of the pillars, you don't need to find them for the quest giver.
A Gift From the Gods - Completed the quest and received the mace. Can the quest item flag be removed from the armours? I'd like to keep them somewhere else instead of lugging them around.
That was the original plan, not sure what happened to it. I'll have a look.

A minor bug I found: During Off the Record, when you escort Manus to his destination, he says "I know you're going to get paid, but here's a ring as a bonus." He doesn't give me the ring, though.
Thanks, I'll fix it. Either I forgot about it or the script lines on that piece of dialogue disappeared. It happens. Really annoying. In fact, when I was improving all sorts of quests for the V2.0 release, multiple script entries on dialogue randomly vanished, breaking the quests. Luckily it was all sorted out before the release.
Since you asked... I've long thought the first Babysitting location could be changed: bears are just a bit much to handle at L1 (I realize you don't *have* to do it at L1, but still...). How about someplace with, say, goblins?
Maybe. I finally got the quest working exactly as I want to and I'm a bit hesitant about changing much more about it.
Oh, and I'm sure you've seen that this mod is marked as "needs TES4Edit cleaning", too.
Yeah. I cleaned the mod before, but some minor things were left after one of the updates. It'll be cleaned again for the next update.