There are were three options, 66Sprinters is a fourth.
Bear in mind that the 250 is exactly 1.666" taller than the 200 with the same engine mounts.
1. If its a 1967, you'll be okay with a direct mount 250 and a the stock base with an aftermarket thin top. There were two differences in the 1967 engine bays to allow the 155 hp (aprrox 99 hp net) L code engines to fit the later engine bays, so 1967-1973 Mustangs might differ in that the L code was technically an option from mid 1967, as the 250 was orginally a Fairlane pickup/Ranchero option which was also added to the Mustang about the time Ford listed the various 302 engine otions (200 HP 302 2bbl, 230 hp 4V, 240hp 302 Tunnel Ram option) .
2. The factory solution for the Mustang based Maverick was to use 1971-1978 Maveric 250 engine mounts, which will retro fit to give you an inch less height on pre 1967 Mustangs.
3. The third, other option is Powerband's mods to the engine mounts.
4. This one 66Sprinters.
The other otions for lowing the air cleaner, and not the engine is to
5. use the remote air filter carb hood that Mike sells, which will get close to clearing the hood. That works with his really nice alloy rocker cover.
6. The Fox body T, B and X code air cleaner for the Holley 1946, its nice and shallow
7. The Australian solution on factory 2V 170 HP M-code Aussie Falcons from 1971 to 1976 was to use a special shallow 1.54" by 10.16" [39 by 258 mm] air filter. That will work with a direct mount carb. With the earlier pre 1965 F-O-R-D rocker cover is half an inch shallower, and combined with a low mount air cleaner and carb, you can maybee get a few inches in your favour that way, but make sure the PCV valve baffled and is not inundated with oil.