Have used a 351 windsor stroked to 383 Dart II heads, Vic. Jnr. and a toploader with the 3.25, live axle 9".
This set up gives me more than enough power than I could ever handle.
Think I agree with 'Jack21' on the option he suggested here. But you did ask for the 289. v. 390FE and this I hesitate on giving advice/suggestions on, as I am not aware of cost associated with re builds etc. here.
The weight difference using aluminium heads on the 390FE was interesting comparison with the 289 cast situation.
I can recal Bob Bondurant talking about 351w in Cobras and the use of them at the race training facility. (Kuit Car Magazine in the late 90's There was comparisons made here about weight, handling etc. You may find his article.
Good luck.
Bernie