I like the idea of DA campaign with Alchemy for Act 1, Cornucopia Act 2 and DA for Act 3. I was also thinking long term and if this campaign turns out well, we might want to do them for other combinations like Seaside/Prosperity, etc. I think a good starting point is using Donald X.'s recommended kingdoms for Alchemy, Cornucopia and going from there. Assuming, he is fine with that. Just thinking that might save us a little time. 60 levels is a lot of levels to program. But, if we are to do it the Goko way the first 3 levels tend to introduce some cards and then the boss battle has the cards we introduced. I don't know if we are going to do it that way or not.
It's fine if you want to use recommended sets, but you should know that if I had a way to use them in the existing campaigns then I already did. You should probably think of every 4th level as being in some sense a "boss level," however you are not introducing cards, they have all been introduced, so there's no reason to match how the existing campaigns go.
I said "two or three expansions" but you can throw in main set cards as needed, since everyone has those.
An Alchemy + Cornucopia campaign sounds great. There already is a pure Dark Ages campaign, or maybe I'm misunderstanding there. Anyway pure Dark Ages for act 3 isn't "two or three expansions."
I would start small, just make a one-act standalone campaign. Twenty levels, get it done, learn as you go. For sure people could make a three-act 60-level campaign afterwards.
There are various ways to try to do functionally thematic campaigns. You could decide to do a campaign where there are no attacks, or every level has a treasure and VP card, or cards that interact with the top of your deck are pushed, and so on, and then pick expansions that best do the job for you.
Zaps are part of the definition of a level; decide how many free zaps you want.