I'm not entirely sure about the idea of penalizing her gold output yet -- as much as poverty is part of Reimu's character, it's also an issue in game design that players tend to dislike penalties. Ultimately I'll have to see how she develops as a civ.
A thought would be to have some way to enable the penalty if you want it, but otherwise leaving it out. I know ViceVirtuoso had his spoiler Madoka civs disabled but able to be enabled in an older version of the pack, so maybe there's a way to do that here to whatever applies the penalty?
A Tourism-to-gold/faith conversion may be possible -- there is a Player.GetTourism() Lua function I can use to find out how much Tourism Reimu is generating per turn, and I can give her gold and/or faith in proportion to that, much like the Moriya Shrine converts faith into science.
Another idea I've been strongly considering is having the Donation Box add gold/faith from trade routes -- specifically, producing bonus gold/faith for every trade route connected to the city.
Tourism seems like the best way to allow for a "peaceful" money source, although it probably can't be a raw Tourism = Gold since that means you could get 1000+ gold per turn from tourism alone, even if it's only in the late game.
The donation box trade route thing also seems very viable, especially since being a OCC civ with no annexing options means there's no real reason to not build national wonders. Hopefully the bonus will still apply to her own internal routes as well, given how those would need to be set up.
A third idea I've been considering is giving the Shrine Maiden units the ability to build shrine improvements. I've got art for a shrine improvement sitting around that I was debating how to use (I don't want to give Reimu a standard UI), but while working on Yumemi I figured out how to make a Citadel replacement. Since the Shrine Maidens would be a Great General replacement, it would be quite possible for them to build shrine improvements instead of (or in addition to) Citadels. So what would the shrine improvement do? While working on improvements, I found out that you can determine if a certain plot has a trade route going through it. So the idea I've been tossing around is that these shrine improvements could be parked on or near trade routes, and generate additional gold or faith for Reimu.
I'd think a shrine should provide faith, although probably not to the extent of a holy site, as well as some kind of military buff since it's a general's tile improvement. (I wouldn't say it should be like the citadel though.) Other than that I'm not sure what exactly it should do. The trade route thing is a cool idea though.
Also my suggestion is to call the UI a Branch Shrine. While the only instance of one in the canon is a Moriya one at the Hakurei shrine, it's the most logical name for a shrine as a tile improvement. It's a shame that you can't do achievements for mods, because having one for making a branch shrine within a tile of Moriya's original capital would be a great one. (Since it seems you'll be the one making Reimu, there could still be some sort of thing between the two.)
So there's multiple ideas I've been tossing around, and admittedly, all three could actually be used. The first could be part of the UA, along with the "get gold from killing units" thing (which I'd like to definitely keep as part of her UA). The second would be part of the EIC replacement. The third would give the Shrine Maidens something to do when not helping fight things, although I'll probably also give them the ability to do something when stationed in cities.
A thought is that if you had all of these things, especially if their bonuses are potent enough, a gold penalty would be next to meaningless after the early game.
I'm definitely very interested to see Reimu in action with all these ideas, especially since I'm a fan of interesting mechanics on OCC civs. (Let's be honest though, nothing will beat Big Boss.)
Also here's the big question:
What would Reimu's colors be given that both Austria and Japan exist?
I've also been trying to think up a good tengu setup (lead by Lord Tenma obviously), but beyond a series of White Wolf melee units (since losing them from an upgrade would be a shame) and being defensive, I haven't come up with much. I suppose culture would be the logical choice of victory but tourism seems like the antithesis of the tengu in canon.
The idea with the wolves would be that they'd be your melee units the whole game, getting new unit names as they upgrade over the course of the tech tree. All instances get a defensive bonus and increased vision distance as well.