I'm curious where you get the data to back up that we are a "small handful" as opposed to the "vast majority". Most users wouldn't put the work in that is required to find this forum. I'd argue that most users won't find David's script (which still only covers a small portion of the settings) either.
This marginalizing language isn't helpful. You have tons of credits with us, so you're still very much in the black I'd imagine. But you must see that this was a debit, and that every single user that has made any settings changes at all has been adversely effected.
To Bill's points above, some clear messaging about the required rework (and some ideas on workarounds) built into the upgrade process likely would have been enough to make your customers feel well-treated, and it wouldn't have been two months of work.
Your small team is amazing nonetheless, and fwiw I'm not angry or whatever. I'm a maker like you, and I chalk this up to growing pains. I hope I'm a productive, helpful piece of the process for you. Afterall, I'm a megasupporter… I want Alfred to be awesome forever.