All of the replies are good.
I make the trip several times a year. As of 4 weeks ago there are still a lot of services out of business due to Ivan. You probably know MS well, so I'll address AL and FL. Stan is harbormaster at The Mariott Grand, up Mobile Bay. He and his wife are sailboat live-a-boards at another marina. Good people! Bayou Ingram (Orange Beach), just before Pirates Cove is a really nice quiet anchorage. Pirates Cove just has the kitchen and bar left and I am told will not rebuild. Bear Point at Orange Beach still has sunken boats in the slips, but you can get fuel there. You do not mention your mast height - because you'll be forced outside with more than 50' at Pensacola Bay. On the inside are many places to tuck into on the ICW. And, once again if your less than 50', I recommend The Village on the Back Bay at San Destin. Call for Capt Ron the harbormaster on 16. They have re-created the French Quarter there. Otherwise you will have to settle for the anchorage at Destin, outside the 98 bridge. Hope your wife likes coastal cruising! You may wish to alternate times on the hook and hotel overnights. Oh, I recommend Claiborne S. Young's guide to cruising the Gulf Coast.