I wouldn't grind the seeds. Not if you want the filtering to ever end

The tea will definitely not evaporate without leaving a trace. Of course towards the end, you'll have to reduce the heat and watch, or you might burn the harmalas and/or the tannins/fats/sludge remaining with them.
Acidifying the tea isn't strictly necessary. It can help the alkaloids move into the water quicker, but i'm pretty sure it'll work without - maybe boil the seeds for a few hours more. I know it's doable without acid for mhrb, don't see why it wouldn't work for rue seeds.
Idk about the alcohol thing. Harmala freebase doesn't dissolve very well in anything including ethanol, but since you'd have some salt form, maybe it would work better.
Tbh, if you want foolproof, why not just boil seeds for a few hours, strain the tea, let it sit for a day or two, pour through a coffee filter, add a base, let the harmala freebase settle? I know you said you don't want a pure powder, and this is nearly pure powder. But i don't think it gets much more fool proof than that.