On your questions I have some feedback that may or not help you.
We are loop veterans. our goal was not to rush things so we took two years to complete..
On the boat we set some requirements.
Your going to be living in it for a year or two so find a boat that you live in.
My wife said two heads with two staterooms.
Also a large galley with full size home style appliances.
Also you need some room to spread out. No matter how well you get along you still cant be sitting two feet apart forever.
I wanted a large ships style pilothouse with heat and AC, and a watch berth.
Our boat is a 50 footer with 17' beam and 6' draft with 17' air draft (no flybridge). We did find that 50' was an issue at some marinas as was the 17' beam.
Unless you can afford to stay at marinas every night (east coast is 2-3 dollars a foot) your going to be on the hook half the time. The boat has to be setup for living on the hook. Good heavy anchors on bow and stern, you don't want to swing out at night in a river channel. A large and very good inverter about 4kw, and a big bank of 8D batteries. A diesel generator about 8-12 KW will run the AC and an all electric galley. A small night generator of 2-3 KW would be good.
You also need a backup battery for the pilothouse to run the electronics.
Now about the boat, 17' air draft is good and you won't have any problems. Just remember to put down your SSB, VHF, and AIS antennas when needed under bridges. 6' of draft is tight in same areas. We grounded several times. That's where twin engines come in handy. I would recommend 5' draft for anyone else. Don't forget a full set of spare parts for EVERYTHING.
A shallow draft of 5' will not ride as well in the gulf, and don't let anyone fool you into thinking the gulf is easy. You could have flat seas in the morning, and 8 footers in the afternoon with wind changing directions. Any way you do it you will have to take at least one overnight run to cross the gulf. If the weather forecast says 2-3 footers it could mean 4-6'. The east side of the gulf is very shallow ten miles out. To be safe you need to run in 40-50' of water.
Also on the ICW the markers are sometimes out of location or just missing. Some people run too close to them, and hit them. Make sure your charts are up to date every month.
We settled down to an easy 50 miles a day most of the time. If (when) you get bad weather just drop the hook and call it a day. DO NOT try to run marker to marker with your radar, remember that markers may not be correct. Also running at 6 knots in the pitch black with 30 knots of wind, and raining sideways is
stressful!
Get cell phones that you can turn into hotspots for email, looking up marinas, and ordering parts. Verizon or AT&T have good coverage and unlimited data plans. Get a new laptop with built in 802.11 wireless.
I am not a big believer in autopilot for the ICW and rivers. Nothing runs straight on them. For the great lakes and gulf you could use one. If you do run on autopilot make sure you have you radar and AIS alarms set to at least 10 miles. Someone MUST be at the helm at all times. You wouldn't believe how many collisions have occurred because the operator went to the head or made a sandwich.
I think you said you live in Detroit, if so take your boat out on lake Erie in bad weather to make sure you can handle the boat, and you and you wife can take the weather and seas.
OH I almost forgot you MUST have a good dingy. We have a Boston Whaler, but any good size inflatable will work an outboard motor. Don't forget the davit to get it on and off the boat easily.
Make sure your wife can operate the boat if you fall off or get sick. Also have a MOB plan and do a few test runs to make sure everything works. Invest in a good EPERB system. The automatic inflatable PFDs work best, but you have to wear them anytime someone goes on deck. Both of you need to practice docking and handling the boat in close quarters.
Get a USCG Safety Inspection and have them check and test Everything. It could save you life or your boat.
Unless you want to hire me and an engineer as fulltime crew