The arguement about long stroke and better low-rpm torque torque is a wives' tale.The only grain of truth to it is that a long stroke engine requires more cam duration at the same rpm.If you halve the stroke and don't change cam duration,the engine will be happy at twice the rpm (provided all other things are optimised to suit that rpm).That's no secret,and I can find reference to this that was printed 90 years ago.
You're still only going to get about 70 ft-lbs of torque from a 1000 cc engine,but within reason you can have that torque at any rpm you like.The maximum valve size you can fit in a small bore can be a limitation at high rpm on a long stroke engine.
Flywheel inertia does more than just give you a slow stable idle speed.If you haven't got enough flywheel inertia and/or camshaft/camwheel inertia it can play havoc with valvegear acceleration.That can lose you a big heap of power and torque.In one instance,Jerry Branch dyno-tested an engine (1/4 of a Chevy engine) that was expected to make 100+ bhp and it didn't make better than 35 bhp because the crank didn't have enough inertia.You'll find it mentioned here in motty's quote,about 1/4 way down the page
http://www.gixxer.com/forums/archive/index.php/t-61151.html
Engine speed and torque aren't constant throughout the cycle.Most of the useful work is done between TDC and 45 degrees ATDC on the firing stroke.Even with a reasonably heavy flywheel in a twin cylinder engine running at 6000 rpm,that can be enough to instantaneously change rotational speed by 5%.It doesn't sound like much,but it happens quickly with severe acceleration.It happens when one intake valve should be opening at a constant speed and when one exhaust valve should be gently closing on its seat.
In the case quoted,increased crank inertia would have improved torque and power by about 200% increase.
Jack Wilson knew this when he built the engine for Johnny Allen's speed attempt in 1956.The crank weighed 50% more than a standard crank.
A light crank is good when you're accelerating in the low gears,but not so good after that.