For 1968 the Continentals had 2 engine options.
the 462 ci MEL Series (Engine Code G) or the more common
460 ci 385 Series (Engine Code A). The engine code is the last letter in the serial number, if you still have the car.
The 460 would be alot less expensive to rebuild since Ford made a ton of those motors and preformance parts are readily available. I would even be willing to bet that you would spend just as much making a 302/351 put out the 485 lb-ft of torque that the 462 came with from the factory (or the 500 ft-lbs. that the 460 was rated at for that matter!).
Just my 2 cents, but it would be really cool to see an old Lincoln big block come back to life.
As for the transmission: Typically the 462 would have come with the Dual Range Cruisomatic (No better than a boat anchor with its cast iron case, in my opinion) and the 460 woud have come with the C6 (with what should be an aluminum case)