For you high-rpm 331 or 347 guys or those of you with 351-408 cubic inches, you'd better get some serious manifolds up on top of that mill. Some of the EFI favorites include the Edelbrock Victor 5.0 intake, the Trick Flow Specialties "R" series upper and lower for 8.2-deck motors and the TFS 351 EFI for the 9.5-deck blocks. Box-style intakes also work quite well with strokers. Remember that your engine now requires a lot more airflow than a motor that is smaller. Consequently, your engine at 3500 rpm is probably drawing the same amount of air that your old, smaller motor used to at 6000 rpm. Once your big-rig mill wants to rev, better make sure you've got plenty of runner and plenum to feed it. It you don't, you'll wind up with a motor that falls right on its face thousands of rpm below its potential peak horsepower.
Carbureted setups are a bit more intricate. Low-rise dual-plane manifolds are pretty much done at 315 cubic inches. It is practically a necessity to run a high-rise dual-plane manifold on any stroker motor with a good cam. One intake manifold that we've seen work great on the street is Edelbrock's Performer RPM. There are others out there that are similar, and work just as well. High-rise dual planes fill the cylinders nicely at lower engine speeds, and offer great top-end charge.
When it comes to single-plane manifolds, the Ford Windsor is a difficult engine to feed, particularly the low-deck (8.2-inch) 289s and 302s. This is because the symmetrical intake ports require manifold runners to be of unequal length. The middle four cylinders suffer from very short runner lengths, and therefore, make cylinder-to-cylinder feeding more difficult, particularly with cylinders number 5 and 6 feeding off each other as they fire sequentially. It is very important to ensure a good distribution of fuel and air to the heads, but with varying runner lengths, you'll have to make some sacrifices (but don't worry, power isn't usually the biggest).
Most carbureted tuners, from personal experience, prefer to put a larger carb than what is considered normal on the small-block Fords. A perennial favorite is the Holley Double Pumper. Contrary to what you've read in magazines in the past, this carb works great on everything from high-winding 306s to stout 408s, and even on automatic applications. If you want to make good power, and don't want your street/strip 331-347 to be soggy, start with a 750. An 800 or 850 would be the natural leap upward, should you want to swing the tach into the far end of its dial or make your 408 happy on the street. Remember that booster signal is what makes a carburetor work.
If you've got a healthy cam with a good cylinder head and intake combination, you'll have some great under-carb low pressure that will make for a crisp and responsive setup. A good place to start with jetting on a 347 with heads and cam is 70s in the front and 80s in the back (stock 750 jets). Everyone talks about fuel pressure, but the most important thing to look for is volume and pressure drop. Maintain at least 6 psig in the lines and use at least a 3/8-inch or -6 AN hose for a feed. The most efficient setup uses a multi-port regulator with a return line.
Because a stroker engine's volumetric efficiency is unlike that of the smaller engine that it is replacing, it is important to tune an EFI system properly. Timing and fuel curves locked into your EEC-IV work great for a stock 302. But with a slew of new airflow and fuel consumption characteristics, it is important to tune your stroker motor accordingly. Of course, a mass-air conversion is necessary, as is a step up in injector size. Pro-M and C&L (Vortech) mass air meters work great on naturally-aspirated and forced-induction applications. Of course, it is necessary to have them calibrated to the injector that you will be using.
A set of 24 lb./hr. injectors is sufficient on 315s and 331s that are mild in nature. But to be safe, a set of 30 lb./hr. injectors with a matching mass air works better, and on most 347-377 naturally aspirated applications. An octet of 36 lb./hr. injectors will feed any hungry unassisted 408, and anything 347 or smaller that will use a small supercharger. Once you start getting into hairy combinations such as Thumpers with 427 strokers, you'd better look into stand-alone fuel management with 160 lb./hr. injectors. But for most of use street guys, the affordable and readily available line of fuel injectors from Ford Racing will suffice.
Ignition
Believe it or not, the stock EEC-IV ignition system is strong and accurate enough to handle just about any Windsor-based stroker motor. A good set of wires combined with a quality coil can zap just about any air/fuel combination present in a small-block Ford. Of course, as with non-stroker applications, you'll want to look at some of the capacitive-discharge ignition systems for use with forced induction or nitrous. MSD, Crane, and Holley Annihilator all offer great boxes that will augment the firepower of your EEC-IV. Other ignition upgrades, such as the Davis Ignition Dyna-Mod will also work. Again, an ignition upgrade is nice, but not entirely necessary on naturally aspirated stroker applications.