The 200 and 250 six have an integrated intake manifold that's cast as part of the head. This is your real power limiter in these engines.
Classic Inline makes the aluminum cross-flow head posted above... if you want to spend $2,000. I've also heard of people getting friendly with a fabricator, cutting off the integrated intake, and repurposing a set of Offy manifolds to do sidedraft Webers.
Also, pay attention to what year engine you pick up. The bellhousing bolt pattern changed from year to year. IIRC, sometime in 1965, the bell housing changed. The early engines are drilled specifically for a bell housing that will only fit a 3 speed trans and late 1965 (and later) engines will accept a bell housing that is drilled for both 3 and 4 speeds transmissions, including the top loader. This really opens up your transmission options.
A friend owned a 1965 Mustang with a 200 six. No modifications other than a retrofit Pertronix electronic ignition. Being a small bellhousing '65 engine, he was stuck with an unreliable and scarce 3 speed manufactured by an English company called Dagenham. When he purchased the car, the transmission was dead. While he was having the trans refreshed, he yanked the engine to do some detailing and have some head work done (hardened seats so he could run unleaded gas). Putting it back together, we found the block cracked between the freeze plugs. He picked up a '66 engine (for free!) and that's when we learned about the differences in the bellhousing bolt pattern. Since the trans was just refreshed and he didn't want to scrap it to pick up something that would fit the '66 engine, he decided that he'd just find a small bellhousing '65 engine and stick with it.
In retrospect, that was his biggest mistake. The 3 speed ended up needing yearly rebuilds. The failures were always gear related and he had multiple individuals rebuilding them, so it wasn't the same guy making the same mistake again and again. Looking back, it was probably something bigger, like case distortion or a casting problem, and he was just treating the symptoms of a larger problem. All in all, he had it rebuilt at least 5 times in as many years. Anyway, had he kept that '66 engine and picked up a four speed to put behind it, he'd probably still own the car.
As it was, he ended up selling the car, 200 miles from home with a busted transmission, to the owner of an auto electric business who restored Mustangs. Being a rust-free and otherwise clean car, he purchased it on behalf of his dentist with the intent of just throwing in a 289 and auto trans that he had laying around.