Given the same heads, cam, induction and exhaust, a smaller engine will usually make more peak HP than a larger one, because of less internal friction. But the bigger engine will make more torque because of the extra cubic inches.
If you compare a stock bore and stroke 427 with a stroked 482" version, the difference in peak HP will not be too much, and of course the bigger engine will make its peak HP at a lower RPM. In terms of torque, the 482" engine will make LOTS more than the 427. The additional torque will result in more area under the HP curve. In the same car, with the gearing adjusted correctly for each engine, the bigger cube engine will be substantially faster down the quarter mile.
For FEs in particular, one thing I really like about the stroker kits out there is their use of BBC rod journals and bearings. IMO the stock FE rod bearing and journal is a weak point of the design. Going to the smaller diameter journal of the BBC reduces bearing speed, and more importantly the extra width of the BBC bearing has more load carrying capacity than the narrower stock FE bearing.
I wouldn't get too hung up on the bore and stroke ratios, or things like rod length or rod ratios. Power gains and losses from these parameters are second order effects, compared to cubic inches. If you want the most power, build the biggest engine you can.
Jay Brown
1968 Shelby GT 500 Convertible, 492" 667 HP FE
1969 R code Mach 1, 490" supercharged FE, 9.35 @ 151.20, 2007 Drag Week Runner Up, Power Adder Big Block
2005 Ford GT, 2006 Drag Week Winner, 12.0 Daily Driver
1969 Ford Galaxie XL, 460 (Ho Hum....)
1964 Ford Galaxie 500, 510" SOHC