changing either drive or jack shaft separately is not a problem.
sprockets can be aligned...............if you have a reasonable method to make correct spacers. You also need to have the wide two bearing upgraded bearing mounts.
on the jack shaft the biggest conundrum is the brake disk. The brake disk with splines is expensive and then you have to remount the caliper. Pain in the rear. I have converted a number of the 013/014 kits to splined shafts and used the stock keyway brake disc on the splined shaft, to do that I machined one of the female spline ways in the disc end of the splined shaft to 1/4" x 1/4" keyway, pretty simple. If you live the in the Missoula mt area, stop by and I will do that for you.
1" id heavy wall steel tube from steel supplier will make good spacers, and a band saw and belt sander, you can make acceptable spacers.
if you order all the spacers shown in the TS parts blowup, if I recall, you won't have the correct spacers to get the job done with the older keyway disc. You need to be flexible.