I have two overall options on my rear drive train and disk brake.
One: I COULD go with the idea of the Predyno and have a rotor on my jackshaft.
In this situation, I would have the drive chain on the right side and have the pedal drive separate from the motor drive. I would have a sprocket adapter for the hub of course...
TWO: I could also use a shift kit and replace my rear hub with a disk brake one.. At this point they would amount to about the same cost, but with the shift kit I would need to weld on a caliper mount. That could pose a problem seeing as how I have an aluminum frame... So I may lean toward the jack shaft brake for that reason.
For the motor you're thinkin' of using, I'd go with option three - a combination of both the above & likely what I'll convert to.
Jackshafting these motorized bikes has become pretty commonplace so most of the issues already known, what's less common is doing it with something other then a kit or utility engine. What's particularly interesting about these horizontal CRF clones is not only do they have substantially more HP per cc then the kit & utilities but they also already have gears - which changes the loading on the bike's dramatically.
Already borderline, with one even slightly missed shift & you could blow all the teeth off the rear cogset. Any of the inevitable derailleur hinkiness at all results in rapid wear at best & even normal long-term use, carefully well tuned as it may be - does take it's toll with hairline cracks & hammered over teeth becoming evident eventually.
This example below still only has under two thousand miles, it's (was) a decent quality cogset bought for this, not stock box store or kit stuff. I only ever missed one shift (third smallest, now missing all teeth but the one) & when I say "missed" I don't mean just the actual action of shifting, but the engine engagement. If you're freewheeled anywhere along the drivetrain you need very carefully match engine & drivetrain RPM every time you get back on the throttle or it'll spool up & essentially "neutral drop" the gears, all of the engines torque slamming into them suddenly with dire results;
...not to say it isn't doable - once bit I've never slammed them like that again, but "feathering" the throttle like that to baby the gears slows down your shifting & knowing I can sheer off all the teeth anytime with even a moment's inattention doesn't give me the warm n'fuzzies miles from home. Worse yet ALL of the other signs of wear & imminent failure in that pic have nothing to do with that one minor mistake, it's all just the wear & tear of normal, careful use... and with only a stock 49cc CRF clone;
I'd suggest the disc brake hub you were thinkin' but with a sprocket bolted to the disc mount. They make 'top hat' adapters if you wish both a disc & a sprocket or you could go with the disc on the jackshaft idea, or even just rim brakes as it's the rear... but I'm not a huge fan o'them anymore for a buncha reasons lol
Hope this helped some, lookin' forward to seein' this build
Merry Christmas and Happy Holidays to you too, KC. And everyone who might have bike parts under the tree 
