Well, before you start buying parts, there are some considerations to look at, the most important being what you want the car to do when you get done with it. I'm not sure what you mean by. ".....I would like the engine to be top end...." But one of the first things to determine is if you are going to use it as a local cruiser or a long distance hauler.

Let me start off by saying I thing the 64 Full size Fords are a neat car. They do have a have a major disadvantage THEY ARE HEAVY. It depends on who's book you read and who you talk to but realistically your looking at a car that is pretty close to 4000 pounds in stock trim (you can always find a "feel good figure" but talking to the guys that have actually weighed theirs the figures range between 3800-4100 pounds depending on how there optioned.

My experience is that the majority of the 352/390 automatic cars came with 3.00/3.10 rear gear ratios and many of these cars have been changed over to a taller tire over the years. Your selection of rear end gears will have as much or more of an impact on how you like the car than the selection of engine components. In generalities if you building a highway cruiser, I would keep the gearing in the 3.00 to 3.25 range. If it's going to be used as an around town "impress the locals" car something in the range of a 3.70-4.10 is a fun gear. A compromise between the two would be a 3.50, not too bad around town and livable on the highway, but not really the best of either. What is ideal in these cars is an overdrive with deep gears and while there are a couple of options to do this none are cheap.

Moving on to the engine, the basic 390 is pretty good just the way it is within its own limitation. First off don't plan on a 7000+ RPM engine without spending a whole lot of money. These engines will live for a very long time if you keep the rpm to a reasonable level (personally unless a lot of work $$$ have been put into the bottom end I'd try to limit it to 5500-5800 RPM and build accordingly).

Short Block: I would start with a GOOD basic rebuild, bored only as far as needed to clean up the cylinders, crank turned or polished as necessary, and new cam bearings. I can't stress this enough, the block and oil passages completely cleaned (if you get the block back and all of the galley plugs have not been removed, send it back and have it redone. Keeping the RPM to a decent level and compression no higher than 9:1 cast pistons will do fine. If the engine your building has a spring and button on the end of the cam shaft, convert it to the latter thrust plate (2 holes have to be tapped in the front of the block). Select a cam that makes good TORQUE in the RPM range your going to operate the engine at. There is always a lot of discussion about oil system mods to the FEs (opening up oil passages, restricting lifter galleys, high pressure/high volume oil and on and on and on) MY own personal opinion is that the stock system is fine AS LONG AS YOU KEEP THE RPM BELOW 6000 RPM. The major changes I would recommend are in the oil pan area. The 64s use a front sump pan, and under hard acceleration the oil tends to move away from the pickup. Pick up a pan with a baffle (PAW sells a cheapie chrome unit with a pretty good baffle in it for about $50) and use a windage tray with a stock (NEW) pump and you'll be fine.

Heads: I think I heard it put best this way, " There are no bad FE cylinder heads, but there are some that are better than others". Just keep in mind that generally the bigger the ports and valves the more power it will make on top end at the sacrifice of torque at bottom end (this is where the weight of the car and the gears you choose really come into play). There has been a lot of discussion on the need for hardened seats when doing heads. In this case your building an engine to move a 4000 pound boat yes it needs them.

Induction: Look for something in a good dual plane design that makes power in the RPM range the engine is going to be running in. Even though when you do the math a 650 CFM carb is enough for the engine, my experience is that 750 CFM carb makes it a little more fun.

Exhaust: The stock log type manifolds SUCK and this is where you can make one of the biggest improvements in the car. You have some choices in headers, but not a lot. There are a couple of companies (Crites comes to mind) that make both long and short header to fit these cars. At the bottom of the price range your looking at plain steel (non-coated) for around $350. BY the time you have them coated/plated your in the $500 range, and you have a set of headers with all the normal gasket blowing problems associated with them. If you go this route, I would recommend using the copper flange gaskets. Another option is to use factory cast iron headers. These came in 2 versions a short set and a long set. The long version made better bottom end torque, but sacrifice a bit of ground clearance and are pretty heavy. They come up on E Bay on a regular basis and go in the $700 range. The short version is lighter and better on ground clearance and usually go for around $500.

Ignition: Defiantly upgrade from the points. Of course one option is the aftermarket. Another route (if you can follow a wiring diagram) is to use a stock motorcraft ignition system. It would also be a good time to upgrade the electrical system to an alternator.

Finally, if your going to just cruise the car normally the stock tranny will likely be OK. If your going to jump on it on a regular basis, I would also start looking for a 67 and up C6.

Hope this helps.