I'd say Yes, And no to keeping the AFM.
Look at things like sound, nothing beats straight off the side of the motor.
Look at extra piping. That's a restriction, minor, but still a restriction.
Then you've got 6 filters vs 1 filter.
Basically, you have to look at how much you're prepared to spend.
I know of only one ECU (Although, I bet there are more) that do a map crossed with a tps tune for multi throttle bodies. And the ecu I know of, is at pretty cheap price too.
But, then you'll need a full tune.
And then, what gains will you get from the 6 throttles + full tune?
Might as well pull the the head at the same time, port it, cams in, etc.
But then, big expense, not a "huge" gain. Are you planning on going turbo later on?