Hi Crustang so this might be a good time to define the goals you have for your 1966 Mustang Coupe such as is it going to be a daily driver Etc. To start the 1973 Head that you have now is all ready much better Flowing than any of the pervious 1963 1/2 to 1968 Small Log Heads that were originally used in the stock early Mustangs, and that is also even if they were also fully Ported with the Bigger Valves installed. For Mods your stock 1973 Head doesn't have the Larger 1.75 inch Intake Valves that Ford started using in all the 1977 and up Large Log Heads so that needs to be taken care of. You could even go up to a 1.80 or maybe a 1.82 Inch Intake if you need to replace all the Valves anyway the cost won't change that much if at all and most will also use the bigger 1.50 Inch Exhaust Valve for some more added Flow. You will need to have the valve guides checked by your local Machinist and replaced if they are worn beyond the specs. The machine shop at the Bare Minimum should do at least a 3 Angle Valve Job or better still is a Serdi Radius type Valve Seat or 2nd best to that is to do a 5 Angle and then Hand Blend them with a Jewelers File, and install the much better Positive Sealing Valve Guide Seals. Use a Bowl Hog and open up the Valve Bowls and hand Blend them into the Ports, Narrow the Valve Guide Bosses into a Tear Drop. Plus depending on your Camshaft Pick you will also need to use the Valve Springs that the Cam Suppler recommends. The Pocket Porting and hand blending of all the Valve Bowls is going to be the Best Bang for the Buck and the Time Spent. You can also do a full Exhaust Porting too, and some like me will use a Center Port Divider. Are you Planning on using a set of Headers?
I don't know what Carb you have right now or what you would like to use on your Mustang. But since you do have the larger Log Carb mounting Hole it would be good to take advantage of that by using a minimum of one of the larger late model 1V Carter Type Carb's. If you plan to use a Big 1 V Carb this is a good post on making a Carb Spacer to use with stock Throttle Linkages on a 200 Six with Large Log Head used in early 1960 to 1968 Falcon, Comet or Mustang Application’s.
https://fordsix.com/threads/carb-spacer-for-large-log-head.82758/
There are also a number of the 2V Carb's that can be installed on a Large Log Head as well as some Multi Carb Combo's, the very best way is to do the Direct Carb Mount hands down this will produce the most power, however you can still can get decent results with a lower cost by using one of the better 2V to 1V Carb adapters such as Vintage Inline's (about the very Best) or there are several others. If you go that route you can also open up the Log Heads intake Carb Hole to a 2 inch from its current 1 3/4 inch size there are some people that even gone up to 2 1/8 inch opening be sure to have at least 3/16 to 1/4 inch of a Gasket sealing surface. Next if you also do a nice Radius on the bottom edge of the Carb Hole opening of 3/16, ¼ inch or maybe even as much as 5/16 inch for those two sides leading into the long lengthwise section of the Log this can help the Air Fuel Mixture to turn the corner into that longest part of the Log. These two above operations can be done yourself with only a few basic tools like a Dremel or other High Speed Grinder if you have access to one or just a 1/4 to 3/8 Drill and some good Bures or Grinding Stones.
The stock untouched Large Log Heads are usually 62 CC's but you should CC yours so you know were exactly were your starting from. Generally it will take roughly a .075 mill cut for most of the stock untouched late model large log heads to get them down to a 52 CC Combustion Chamber when used with a stock type 6.5 CC Dished Piston.
Will you be rebuilding the Short Block also? What Compression Ratio are you planning to run? In the US at locations at or near to Sea Level you can use up to a 9.2 to 1 Compression Ratio with the cheapest 87 Fuel and go more if you want to use Premium Fuel. The Camshaft you want to use will also be part of this to know what Dynamic Compression Ratio you can run.
Note for reference that the 1963 1/2 to 1968 200 Six short blocks (as well as most of the later model 200 six's) during a rebuild end up going to a .020 to .030 Over Bore. One Combo you can use is the stock 6.5 CC Dished Pistons or also with the Flat Top Piston's (if you can locate them) and than go to a Zero Decked Block. Used with a FelPro and other brands of Composition type Head Gasket's that we have today (they will have a .050 Crush Thickness), you would then need to Mill the Large Log Head down to a 52 or 54 CC Combustion Chamber (depending on the Piston Type you use) this would bring you right up to 9.2 to 1 Static Compression Ratio (C.R.) and it would then have a .050 Quench Distance. The Stock 1963 1/2 to 1968 Ford 200 Six's mostly all had these 6.5 CC Dished Pistons except for those models built with the California Emissions market (the original Factory Ford Pistons had a Compression Height of 1.511). On average this had the Piston Top setting down the bore at .019 and with the stock 200 Six Small Log Heads that were usually at 52 CC's and their stock thin Steel Shim Head gaskets (about .022 Crush Thickness) they would have a Quench Distance of .041 with a C. R. of 8.7 to 8.8 to 1.
The problem is that most of the Ford 200 Six replacement Cast Pistons will now only have a Compression Height of 1.5 putting the Piston Top even farther down the Bore at .030 and this requires a lot more block Milling to bring it the Short Block back into spec again. I have recently found out that the Australian Spec 200 Six Pistons (with a 6.5 CC Dish and also the Flat Top's) are available easily here in the US for about the same price as the US spec Pistons, this can save some cost in not needing to do so much Block Deck Milling. Those Pistons have a higher Compression Height of 1.530 so this should bring you right near a Zero Deck Height with the stock Block Deck Height or else would be very close. It is a good ideal to measure your Pistons Top to Block Deck Height on both the number 1 and 6 Cylinders when at True TDC so you know where your starting at. Another option would be to Mill the Block deck so that the Pistons are at .010 above the block deck than that would get you right back to the much better Factory 200 Six Spec of a .040 Quench Distance and the head also won't need to be milled as much either.
I don't know what you have now or plan to use for a Distributor but there are several options that can work well, except for the old Load O Matic type which isn't very suitable for a Higher Performance Build up. You maybe be better off going to a stock 1977 to 1983 DuraSpark II Electronic set up if your car happens to also have the Factory Stock Power Steering since the HEI's and DUI's won't fit with the stock Ford power steering. The DuraSpark II's can be upgraded further with an MSD control Box too. Best of luck and hope this is of some help to you in Planning of your engine build up. Edited