I would recommend taking the engine out completely, and sending it to a machine shop. They can make it look brand new again, and if you want, they can strenghten the internals of your engine if you plan on adding any extra power. Also, new wires and hoses etc makes it look very good. A nice chrome carbureator will set it off nicely.
As far as your 2nd question, I would redo the interior 1st, and then the paint, but that is basically personal preference.
Good luck! If you do not know much about mechanics, I do suggest paying the extra money to have someone else do the hard work, that way it will be done right, and last a long time.
Beautiful car to restore by the way. Good Luck

With any restoration you always work from the inside out. . . Paint is always last.
What I would suggest is you watch Speed Channel especially Chop Cut Rebuild or Dreamcar Garage both good and informative and especailly inspiring then there is also another great source of information at Jay Leno’s Garage online!
You are right about flushing and replacing liquids in the engine and trany and also re-pack the wheel bearings and check your brake lines for deterioration, sitting is not a good thing for a car to do.
Sounds like a good father son project, my dad had a 66 Belvedere 2 door coupe and mom had the Dart GT, both great cars.

FYI- It’s going to be a big project, and I guarantee it’s cost a lot more and take a lot longer than you initially expect.

That said, start by stripping all the trim and interior off the car.

Assess the rust situation and begin repairs.

If you’re not experienced, you should at least make friends with the guys at a good local body shop and start chatting them up. Maybe you’ll get lucky and find a guy who’s into Mopars and has specific knowledge about the make (like the fact the right side wheel lugs are left-hand threaded; and early 318’s (up until ‘66) had the scalloped valve covers- later 318’s have straight valve covers, and the parts don’t interchange). . . Etc.

Pull the motor and tranny and start disassembling, cleaning, de-rusting, etc. . . . . . . . . .

After stripping, you should treat surface rust with phosphoric acid (commonly sold as a product called “Duro Extend”).

It converts Iron Oxide to Iron Phosphate, which seals the metal and can be painted over.

Make sure all the structure and floor are solid. Cut and weld in new panels as needed. Year One is a good source for new panels, trim, upholstery, etc. . . . .

It’s easier to paint the car while apart and the interior’s out, but be extremely careful during assembly so you don’t scratch up a brand new paint job.

Gunk spray or Simple Green along with some elbow grease will work to clean the engine and drivetrain while it’s out. Mask & repaint everything in original colors after it’s clean.

They sky’s the limit as far as what you want to spend and how ‘perfect’ you want it to be. You CAN make it better than it came from the factory, but it might be cheaper to build a time machine and go back and actually buy a brand new ‘66 – lol!

Sounds like a GREAT idea for a father/son project. Good luck!

Before you remove a single item, take extensive photographs of the car. You will need them later for re-assembly. Start with front end disassembly (grill, bumper, wiring, etc. Next remove drivetrain. Send it out for rebuild, or clean-up. Interior is 3rd. Remove dash components,seats, carpet. Etc.

If it is a full frame car, put the body on a rotissary (reinforce and brace it before you lift it from the chasis.

Then take the frame and body for media blasting. You can strip the frame down to just a rolling chasis but, fully striped is best. Put the exposed metal components into primer right away and powdercoat or paint the frame.

Then you can start to re-assemble and upgrade anything you like.

Have fun!