No problem- Put one of the 603's about 6" off the skin, angled toward the center, as if it was a snare drum. Put your kick mic on the open throat, about 4" outside the drum, and reverse the phase on one of them. If it's a big one, put a pad on the 603. Thje real issue with Djembe is who's playing it, and their hands. Rimshot is my drummer, and he's been playing lead Djembe with West African drum ensembles for years, with a series of teachers whose names start with "Baba".
You've heard of talking drums, right, where a message can be sent literally miles on a clear day? Baby, I'm telling you, Rimshot's hands are like the soles of leather shoes, and when he slaps that puppy, it'll blow your head off!
By implication, unless your ceiling and floor are heavily treated, it will also blow your room away. I find that with 18" of compressed fiberglass insulation and sound board covered with Auralex foam or carpet above it, and carpeted concrete under it, I can actually record the thing without it sounding like a defective echoplex. I don't know how much you know about playing Djembe, but it's the Djembe *player* that determines what you have to do to record it.
Also, Djembes come in many sizes, up to the size of a conga, or even bigger, and the bigger they are, the more of a room challenging thing they are. That's most of what I know. For more, just PM Rimshot. He's probably one of the best Djembe players in the country, and I'm honored to have him on staff. You're welcome, Rimshot.-Richie