Jeep 4.0 in 69 Barracuda
I have built magnum V8 jeeps since 98 and only used magnum factory injection so I get the injection idea but the 4L is over 4" longer than the V8 and makes half the power. It is much too tall to even fit under the hood if there is a place for the length. Why not just put a 94 Grand Cherokee 5.2 in it? Half the work, twice the power and done in a weekend.
I see several issues related to the swap, engine height, engine length, motor mounts and of course, exhaust.
I understand your love for the jeep inline six but unless you are planning on doing tractor pulls with the 69, it seems like a big effort for little return.
I would advise against doing anything with a Dana 44 from a Grand except holding a boat in place, they are junk and explode just looking at them. They make a Dana 35 look tough.
Not trying to bag on your idea, but you seem to have a pretty nice start to a cool 69 fish and I dont get the engine downgrade concept.