Mark,
I met and discussed this trip last night with the guys in Surabaya. Definitely no security issues according to them so i wonder if we are talking about the same place ? This might be a bit further north than the area you mention .
Plan is to fly into Ambon and then get on a local tuna boat which will be the live aboard and tow a speed boat with us. Apparently the atolls - 3 in total and huge are 100 miles south of Ambon so takes several hours to get there. Apparently in November waters are calm so that the best time to go. Atolls are called Luci Para. Apparently Bali guys are also going up there but to spearfish doggies.If we put it together will drop you a line.
Regards