Exhaust, yes, intake.. not completely. I know it's been an issue for people swapping HO manifolds onto Renix heads. It will still work, though. May not even be noticeable.
Yes, the dizzy must stay with the electrical system.
Which generation transmission did you swap in? I don't know if there's a factory pilot bearing to use an older transmission behind a newer 4.0, like there is for a newer trans behind an older 4.0.