I recommended the rpm air gap because its a proven, great performing intake manifold. Im pretty sure you can get it in polished. Yes, you will consume more gas with a 4 barrel, but its really the only way to go with a performance application. I dont believe you can even get a performance intake for a 2 barrel carb. The 550-600 cfm means the size of the carburetor. They range all over the place, from 300cfm to over 1000cfm. Too small and you lose performance, too much and you lose idle quality. A edelbrock would probably be a better choice over the holley for you, they are alot easier to tune. You will not have to change the gears in your rear end for a new trans. To instal a 5 speed, (a t-5 from a 87-93 mustang) you will need: a new flywheel and clutch, transmission crossmember, clutch cable, transmission yoke, and to have your driveshaft shortened. Of course you will also need the transmission! I believe you can use your old clutch pedal, or you might have to switch over to a 71 mustangs clutch pedal i believe. (not exactly sure if you have to and what year if you do) As far as that exhaust, im not too sure. It says a cat-back system, which your car doesnt have. (the catalytic converters which werent made mandatory until 1975) If you do go the t-5 route with a cable clutch, it will make fitting your headers easier. (the mechanical clutch linkage that came stock on 65's and im sure 66's is quite an obstacle) I recommend ordering every magazine about cars you can and start reading.
www.jegs.com check them out, order a magazine (free) all kinds of engine parts and stuff
www.mustangsplus.com You can order a free mag from them too, they have all the parts to do the t-5 swap
http://www.mustangandfords.com/techarticles/5272/ Here is an article on the t5 swap.