Thanks for your interest. I am happy to discuss this topic at length, since this is my hobby project, so sorry if my replies are too long.
Perhaps you may want to join our discord for easier / more detailed discussion.
First, I would like to point out that full event order is documented in 'More info' menu (maybe you have already seen this, I just want to make sure).
Specifically, for 'end turn' the order is, indeed, 'cards, then items, then quest'.
About quest vs item trigger order. As I see, the main advantage of your proposal (quests before cards and items) would be easier understanding by novice players (i.e. less cases of "why it did not work" surprises and frustration). The corresponding disadvantage would be, for more experienced players, symmetrical frustration of 'I lined up end-of-turn effects perfectly, but game ignored them'. For e specific example, just as Model of the Spire can hinder library quests, Ornate Deck can make them much easier. Also, anti-synergy of some item/quest combinations are one of the reasons to pick Black Box item.
In general, I push this game in 'give advanced players more tools / interactions even at the expense of harsher learning curve' direction, so I slightly prefer current order. However, your proposal merits further thinking / discussion, I will certainly consider some changes in this area.
As for relative order of items (such as Pendant of Amnesia vs Sun Shield) -- note that you can reorder items arbitrarily between stages. Unfortunately, this does not help in this specific case, since Sun Shield is triggered on start turn, not end turn.An interesting idea wold be to change Pendant of Amnesia to start turn trigger (so you can, for example, put it after Moon Blade but before Sun Shield to achieve both effects on the same turn).