I've combined Caffeine, as well as Theobromine, with Rue/Harmalas on several, and i do mean several, occasions. I haven't tried Cacao or any of it with Caapi, though. With that said, the primary concern imo seems to be with the CYP1A2 inhibition of the Harmalas, specifically Harmine. CYP1A2 is responsible for metabolizing Caffeine, Theobromine and other things, like my sleep medicine Tizanidine, i use the 1A2 inhibition of Harmine to potentiate my Tizanidine, works well. I've also noticed potentiation of Caffeine many a'times, and have also noticed potentiation of Theobromine. When it comes to 1A2 substrates, when there's inhibition involved, the dosage of the 1A2 substrates need to be reduced, cut in half at the least, especially when consumed either at the same time as or up to about 10 to 12 hours after the Harmalas, that seems to be when 1A2 inhibition is in effect. Whereas if you consume a 1A2 substrate either earlier in the day, or after about 10 to 12 hours after the Harmalas, there won't be any potentiation, that i've been able to tell.
With that said though, i like a little Caffeine, or Theobromine, with my Rue/Harmalas. But i've taken some pretty stiff dosages even on top of 1A2 inhibition, and haven't ever had anything "negative" come from it, although i wouldn't recommend consuming too much Caffeine or Theobromine in general.