Check Mustang Geezers modifications first up. 200 sixes are ultra shallow in the block, but the 69 had a lower hood than before. Consider an air cleaner modification to suit the throttle cables. Then read through this.
I had this dreaded problem on my Falcon 250, and its easy to fix if you are patient. Aussie 2V Falcons had factory 39 mm (1.535" tall) air cleaners just to get them under the hood. The solution is to check how much throttle cable/rod space there is if you drop the aircleaner body down some. (Bring it down futher, in English). There are a whole range of available 1 and 2 and 4-bbl air cleaners to choose from. My old Ryco filter manual lists some US cars down here in New Zeland. They have a three way index which lists them by height, application, or part number. So its easy to get an interchange. If you get a filter too shallow for your housing, you can add a nylon spacer made to make up the difference. That means, as long as its shorter, you can pack it up to the dnoar air cleaner housings required specifaction.
For our antipodean cars down in Aussie/NZ. We have the following sizes:-
A37 60-61 144 Falcon (H=2.205", OD=9.685",ID=7.913")
A55, 62-69 144-170-188-200-221 Falcon (H=2.205", OD=9.685",ID=7.913")
A217(1-bbl) 70-76 200/250 tall block Falcon/Cortina (H=2.047", OD=10.0",ID=7.675")
A224(2-bbl) 70-74 250 2V tall block Falcon (H=1.535", OD=10",ID=7.675")
A391 Dodge Truck Air Cleaner used for Impco LPG carb like mine (H=2.835", OD=10", ID 7.675").
US Ones that have simliar dimensions are :-
A37 No interchange for US, but early slant six Chrysler may fit (H=2.205", OD=9.685",ID=7.913")
A55, Ramber,Studebaker, Canadain Fords (H=2.205", OD=9.685",ID=7.913") A217, no inter change(1-bbl) 70-76 200/250 tall block Falcon/Cortina (H=2.047", OD=10.0",ID=7.675")
A224 no inter-change (H=1.535", OD=10",ID=7.675")
A391 Dodge Truck Air Cleaner used for Impco LPG carb like mine (H=2.835", OD=10", ID 7.675").
Note that I use a big diameter Dodge air cleaner, a very tall air cleaner because I've butchered my throttle linkage to let it fit inside the filter casing. What helps is knowing what the total angle of throttle movement (often 78-80 degrees, or 1.361 to 1.396 radians), the net movement at the pedal (often more than 3"), and the net movemnt of the shaft (can be as little as an inch, or as mutch as two inches or more). Using a piece of string to measure the movement from curb idle to wide open throttle is important. Some kickdown cables for C4's are mounted on the throttle at the driver, or by a long tubular shaft to the trans. It all gets in the way. If you mess with one, the actualtion of the other is changed. If you do decide that you can change the filter casing for a shallower one, then make sure there is enough space to give free movement, or your car could take you for a ride you'll never return from...
I've found that as long as you preseve the throttle pull out in inches, you can shift the throttle and kickdown rods on to a tighter distance from the throttle spindle by a proportional amount. Often if this is moved inwards to the spindle centre by as little as 1/8 " (0.125", or 3.18 mm) the throttle pull out can be decreased by more than 0.175 ", or 4.4 mm). This will ruin your kickdown, or mean you've got an oversensitive throttle. The throttle lever arm then needs to be changed. It gets difficult! Throttle linkages rate 8 out of 10 for difficulty on installations where space is tight.