9” Third member interchangeability…

Nothing wrong with 3.00's with a 460, I run a warmed over 460/C6, 27.7" tires with 3.25's and they are almost too much for cruising over 60mph. In my Ranchero's previous life it had a stock 460/C6 from a '76 T-bird and I installed a 2.50 gear rear axle after the original differential started leaking and having other issues. The stock engine with a Holley 9834 VS carb gave me an honest 17.5 mpg on the highway. The BB 460 will not really care what rear differential you have until it gets too low. Picking a rear gear ratio is like picking a camshaft for the engine, very easy to go too big on the camshaft(or in this case too low a gear ratio) and just ruin the drivability of the vehicle, same goes for the rear gear ratio. Unless you are going racing with your Cougar, I suspect you'll hate the 3.89 gears after the initial smile the acceleration gives you. Just my opinion but hope this helps. Good luck with whatever you choose.

I guess I should elaborate on interchange options. 31 and 28 spline setups run identical gear sizes on the 9”. 35 spline is also the same. The difference is the differential and housing, there are 3 common bearing sizes on those but most oe 28 and 31 spline setups run the most common smaller ones. Then there are some special in-between race setups to run smaller carrier sizes in larger housings. Because the ford 9” is pretty much the most popular setup in existence there are all kinds of combos people came up with over the decades.