Amen, Andy - on almost everything.
I replaced my original auto box with a Tremec 5-speed. My original reason for swapping transmissions was due to the extreme heat generated by the Police interceptor C-6 box. In half an hour of driving (in California), you could have cooked an egg on the trans cover. Ouch!
The manual is smaller in size and more efficient. It generates less heat, and the heat it does generate is carried away by better airflow through the transmission tunnel. The swap is easy (at least it was on my car) as the mounting points are already in place, and no chassis alteration is needed to install a top-loader based manual. It's an easily reversible swap. I've kept the original transmission and torque converter, as I have done for everthing I've replaced on my car.(except the radiator and flex-fan. I threw them out in a fit of garage cleaning. And the diff gears - They went into Mr. Feldman's coupe when I changed the rear-end ratio on my car)
If you plan on driving in hilly or twisty terrain, a manual gives you better control. You get better mileage, better acceleration, a higher top speed and lower revs. Torque is still your friend!
I know it's been said (for years) that 428's are best suited to auto boxes. That might be true if you were to use a modern automatic transmission, but the original, though tough and bullet-proof, is a major source of heat and a waste of power.
Amen, as well, to changing the intake manifold, the heads, the exhaust manifold, the radiator, the fan, springs, shocks - all that Andy suggests and more.
A wonderful thing about the engine and drivetrain is: You can still get EVERYTHING you need - inexpensively! - to shed weight and improve performance! I replaced my iron Intake manifold with the identical date-correct aluminum Police Interceptor manifold, saving (as Andy says) a great deal of weight! I re-purposed my transmission oil cooler to an engine oil cooler, and the difference in consistant running temperature is considerable. Modern Aluminum heads (I used Edelbrock) solve the valve seat problem, save weight, improve performance and engine heat dispersal. A small chin spoiler (nearly invisible, and removeable) also helps enormously.
David - you can easily purchase a "correct" Holley 4 barrel on Ebay (requires time and patience), or buy one a new one. Not only are they still being produced, they also re-condition the old stuff.
Edelbrock, Blue Thunder (and others) make correct aluminum intakes, if you don't care to track down an "original".
Exhaust headers are a custom-fit proposition. As Andy says; nothing will fit without modification. Not a big problem, but it does require an artful professional to be successful visually and functionally. I replaced the whole exhaust system with ceramic coated stainless. Now much more heat goes out the tailpipes, less on the passengers bums.