differences as follows:
219cc between the 9 and the 12 models. 9 model is 984cc/12 model is 1203cc
displacement increase achieved via stroke increase as you mentioned
9 is geared "lower" than the 12. that is achieved via the primary front sprocket assembly. the 9 is a 34 tooth count and the 12 is a 38 tooth count.
all 9's and 12's have the same front pulley and rear pulley tooth counts wtih exception of very early model years.
all XB models have a 5 speed trans. in retrospect 5th gear should have been overdriven...or better yet a 6 speed transmission.
the gearing between the 9 and 12 models equates to the following speeds and rev counts in US measurements:
at 4000rpm in top gear a 12 is traveling approx. 80 miles per hour/a 9 is traveling at approx. 72mph.
the the stock 12 has the factory power valve exhaust system. the 9 does not.
i have owned every buell XB model ever produced at one time or another and in both engine sizes. still to this day my favorite "over-niter" XB is the ulysses. they are all 12 models. my favorite day-tripper is a 9 cityX.
here in most parts of america 75mph is an acceptable large highway cruising speed. a 12 motor feels very comfortable at that speed...a 9 motor is somewhat disconcerting in that it feels and sounds busy....as if it may come apart. i can assure you it will not. how do i know this? relatively low piston foot speed per mile. here's the formula: Piston Speedfpm = stroke x rpm ÷ 6
my personal preference is the 9. you really need to "pull the trigger" on a buell purchase over there before the opportunity passes you by.