If it was me, I'd stick to the cheapest option for sure (I'm only human, right?), but I'm talking on a grander scale. The reason Jeep decided to put V6es into CJ5s back in the day is because a mechanic started transplanting them in place of the F head. People liked the idea, heads were turned, and eventually deals were made. If it was a one-off conversion then I'd say you're right, in that it'd be costly for the power gained. But having said that, if you had, say, 150 people who liked your upgrade and asked for one themselves, then the cost of adapters is reduced significantly.
I'm not really sure about transmission/x-case choices, but I know that most BW/Tremec solutions, i.e. the T5, should bolt onto the Falcon 6 cylinder. The power and torque values aren't extreme either, so as long as you behave yourself then the driveline should hold up OK.
Granted I haven't really thought about this in a lot of detail - I just want to throw it out there and see what people think.
