Little confused here. You have a 2007 classic with stock exhaust, including the cat box. You wanted to remove the plenum and put a Ramair on. If you did this, you would lose power because the tune you have in there won't have enough fuel. But you've ordered a Dobek AFR? If you hooked this up, you could theoretically add the needed fuel to go with your Ramair. But I see no point in putting on the Ramair with the stock mufflers. It's just a big hassle for little power gain after you retune it.
Now, you have access to D&D mufflers? These are 3-1-2 with both mufflers on the right side? With the stock intake, this would be close to the 3 TOR's with the cat bypass pipe and the stock 20226 or better, the 20050 decel tune would probably work. But if you put the Ramair on, you need more fuel and the 20050 decel tune won't work. But your Dobek with AFR+ probably would. I don't know how these AFR systems work - you still need to supply A/F targets - my feeling is that if tuning requires my input, the result would be worse than if I brought it to a good tuner . I would prefer scrapping the AFR and having a dyno tuner tune the Dobek on a dyno. Since most dyno tuners use Dynojet dynos, a Power Commander might be easier for them to deal with.