I've been going with this setup on my 2 Rank 50 ships:

Hull - Invincible
Rigging - Enterprise
Forecastle - Tatanora or Invincible-II
Aftcastle - Invincible-II or Tatanora

This lets me visit 2 of the deep sectors on either ship, gives me high surveillance/favor on one and high retrieval on the other and doesn't take forever to make the trips. With the Enterprise rigging and Invincible-II Aftcastle, a trip to SC21 & SC22 takes ~61 hours.