There is a lot of wives-tale type information out there, but as an engine builder I can offer my two cents:
Bore vs Stroke is sort of a moot point. Given two identical combinations of parts, cam timing events, intake and exhaust velocity and mass flow, bore and stroke won't make any appreciable difference. This exact thing was proven on a dyno many times, but the one particular example I recall was setting using a Buick 455 (huge bore, short stroke) and and Olds 455 (small bore, long stroke). Everything was matched as closely as possible. Both made nearly identical torque and horsepower curves with peaks at the same RPM.
It was long thought that long strokes increased torque because of the greater leverage on the crank. That would be true if the engine were providing torque at 0 RPM, but since the torque in an engine is expressed as a function of power, motion is required. The bottom line is that there are 455 cubes worth of displacement available to provide force to the crankshaft.
Where you find truth in the wives tales is that (for a given displacement) longer strokes lend themselves to low-rpm torque... not directly because of the longer stroke, but because making a long stroke engine rev is an engineering hurdle. Its not that you can't, its rather that it takes a considerable amount of energy to overcome the inertia of the heavy, long legged rotating parts and high piston speeds. It also takes more exotic (expensive) materials to keep things together. If you think of the piston speeds and velocity changes in that long stroke Olds compared to the short stroke Buick, it stands to reason that it takes a lot more energy (and strength of parts) in the Olds to spin it to 6500 RPM. In a nutshell, its not that long strokes make more torque, its just that the physics make it a wiser choice to engineer it for lower RPM.
The other main reason for long stroke/small bore engines disliking revs is due to valve size. Small bores limit the amount of flow area you can achieve, therefore limiting RPM.
For this reason, I tend to chose large bore, short stroke engines for several reasons. Mainly, they can be equally competent stump-pullers as their long-stroke brothers, but if plans change in the future I'm just a cam and head swap away from bigger power.
There are reasons for chosing long stroke, however. Depending on chamber design they tend to be less likely to detonate and the smaller surface area of the cylinders means that parasitic friction is often reduced.
The argument for inline versus Vee and all of the vee angles possible is mostly due to reliability and harmonics. Higher RPM harmonics can not only kill reliability, but power as well. If the engine starts wasting energy on moving the engine around on the mounts, its losing it at the crank. Again, though its a trade off. Inline 6s are typically built with 7 main bearings which makes them very strong and reliable, but the additional friction and inherent harmonics of the longer crankshaft make them less suitable for higher RPM use. The 60* V6 is a much more stable platform for higher RPM but typically only has 4 main bearings and a crankshaft that holds two rods between mains instead of one.
Working at a transmission shop, I see the problems of the inline six vibes all the time. The Cummins diesel wreaks havoc on transmissions. Since it pulses every 120 degrees (and since they are rather violent pulses) it makes transmissions vibrate apart. A good example is the NV5600 transmission that was available behind both the Cummins and the Duramax. Behind a Cummins I see a lot of them around 150-160k. Since the Duramax came out I have seen one in my shop.
