5.7 swap

As far as MDS it's not really an issue if your engine has it because you can always disable it one way or the other (swap the special lifters to standard ones and get plugs where the solenoids go or just leave the solenoids in but unplugged). You may still be able to use MDS if the whole drivetrain gets swapped in, but I'm not sure about that. I'm fairly sure the computer probably needs a speed signal to activate the MDS system, but if you keep the trans with it you might be able to keep everything intact, though only the later engines (06+) use MDS and I think most people prefer the earlier engine computers since they are easier to tune. Also, as the years went on I believe more chassis components got included in the computer control (like wheel speed sensors and other stuff not directly engine or trans related), so it's a lot more trouble to use them in an engine swap unless you want to go all out and add stuff like wheel speed sensors to an old car.

As for a trans I think you'll probably have to cut some pretty big holes in the floorpan to fit any modern transmission. I would think the truck trans might be even bigger than a car one.

You look like you're on the right track for the other parts though. If you keep the truck trans you won't need the flexplate, but I believe all the Hemis use passenger side starters from the factory, so you'll either have to use factory manifolds for the exhaust or get custom with headers.