georgia pony, pony66, the 250 is a good solid engine that can make a lot of power, just like the 200 can. pony, the problem most people have with hood clearance when swapping a 250 into an early mustang is that they forget to drop the front of the engine about an inch. it is easy to do you just drill new holes in the mount. a better way to go would be to use maverick 250 mounts. you will have to drill a couple of new holes to use them, but they will drop the engine the needed amount also.
as to using the early 170 head, the later 200/250 head is better as is has the larger log volume. granted it does have large combustion chambers, but you can mill the heads to get the compression ratio you want. just remember to mill an extra .025" when using composite head gaskets as they are that much thicker than the original steel shim head gaskets.
as to having to use the 250 to use a V8 transmission, not true. there are adapter plates you can get to run the T5 behind a 200. the 67 and later bell housings are already set up to use the 3.03 top loader three speed, though you need a 66 and later dual bolt pattern block to use that bell housing. if you are stuck with the 2.77 bell, you can still use the T5 or even the 3.03 or top loader four speed with the right adapter plate.
as to clifford performance products, when jack clifford was there, they were the source for performance six cylinder parts and information. and their customer service was excellent. however since jack died, they have gone down hill. the place for ford six performance parts now is classicinlines.com. mike has done something that clifford has been talking about for more than 20 years, but never did, come up with a new aluminum head for the ford small six. classicinlines also has a cylinder head service where you can send your stock head for simple rebuilding, to having it modified by guys who are experts at the ford six head, including having adapters installed for putting on two barrel carbs if you want.
classicinlines also has performance camshafts ground by clay smith that were designed for the ford six, and not just an off the shelf design. you can also have classicinlines have clay smith custom grind a cam for you if you want. i dont remember if there is an extra cost for this or not, ask mike at classicinlines to be sure. mike is also developing a new full roller rocker arm system that is inexpensive, about $350 is his target price as i recall, and i believe they are adjustable. mike also has headers not from hooker though, his own design that actually fit properly. he may still also source headers from pacemaker, an australian parts supplier.
so check out
Classic Inlines Performance Parts - Home and dont forget to pick up a copy of the falcon six cylinder performance handbook available from them. a lot of good information in the book.