I just got done rebuilding a 460 in a 1976 Continental Coupe (not a Mark), so here are a few things for you to chew on.
I don't know how experienced you are at building cars, but from my personal experience (stupid mistakes), don't buy anything until you have your complete build carburetor-to-oilpan thought out. It will potentially save you a bunch of money. Opening up your engine and determining if you will reuse the short block or go with a stroker is obviously the first priority, and will affect head, intake, and cam choice.
I personally didn't want headers on my Lincoln due to clearance issues and if/when they leak you might have to raise the engine to change them, and most of the headers that looked like they would fit were of thin 18 gauge metal (junk imo). This led me to put on a pair of Police Interceptor exhaust manifolds, and manifolds would probably effect power in the 500 hp range, so that ruled out a stroker for me. Higher horsepower higher maintenance headers or lower horsepower low maintenace manifolds, to each his own. I just wanted a decently powerful big car, 572 cubic inches was not my main priority.
I did a full rebuild--30 over 15cc KB pistons, regular performer intake (for a heavy car you need all the torque you can get), mad porter's budget ported d3's, custom street rod cam from Randy Malik. By the time you have a machine shop completely go through a pair of heads--new valves, seats maybe, springs, etc I think you will have a hard time beating Mad porter heads for the price if you are going the iron route. Also take into account the quality of portwork. Does the guy at the machine shop know BBF heads specifically, or is he just a Chevy guy with a grinder? There is grinding, and then there is porting.
A standard warmed over rebuild like I did will make the car noticeably faster and more fun. I am definitely satisfied with it, just don't expect too much performance out of a 5000 poundish car. Laws of physics do apply here. The open 2.76 rear end in my car sucks. Gearing is probably an essential detail in a tank car build, I am thinking 3.25 or 3.50 so it will still be road trip worthy.
If you want your car to have major *** behind it, definitely go the stroker route. Not much more money than a standard rebuild with significant power gains. CarsbyCarl has very competitive rates on shortblocks compared to what a local machine shop would charge, so take a look there or with other vendors if going that route. Stroker would allow you to go to a Torquer 2, but I wouldn't advise going to it on a 460 in a Thunderbird, you will lose too much low end.
Another suggestion--throw out all horsepower numbers when dealing with a heavy car. A 600 hp engine built for a 2800lb coupe will suck in a 5000lb Tbird. Low end torque is where it is at, and this requires a smaller cam, which will reduce high rpm horsepower. Just a trade that has to be made. How often do you really hit 6000 rpm on the street? For that reason, 6k horsepower numbers don't impress me. Torque from idle to 3k or 4k is where its at.
In the end, it all comes down to your budget. Parts add up very quickly. I think you have three options:
1. Do a very standard warming over of your current bottom end. Take off egr crap if it has it, timing chain upgrade, carb, dual exhaust, rod and main bearing change if worn much.
2. Redo the 460 something like I did, decent heads and intake. Makes a fun car.
3. Stroker kit with aluminum heads, torquer intake, headers etc. Will need fat tires and suspension upgrades to have any chance of putting some of this power to the ground instead of up in smoke.
One big thing to think about. Do you put some decent money into it now in kind of a half *** job and then later decide to go the stroker route? That would be throwing money in two different directions. Alway important to consider this before you start throwing good money down.
Just from my personal experience. Hope you have fun and keep us updated.