Oh, I forgot one thing. The primary sprocket. I understand about the retainer, but I thought they both used the same gear, just were retained differently?...
We need to get some terms straight.
The primary gear
is on the right-side end of the crankshaft. It meshes with the ring gear on the back of the clutch. It is held on to the end of the crank shaft via a nut and a lot of torque.
The kickstarter gear set
is made up of a gear that is attached to the kick-starter mechanism, an idler gear that mounts on the end of one of the transmission shafts and the hub gear that was on the back of the clutch basket for the first few years of production.
The counter shaft sprocket
is on the left side of the output shaft of the transmission.
I believe you are asking about the counter shaft sprocket.
The early counter shaft sprockets were a 15 tooth chain sprocket held on by a splined retainer that was bolted to the sprocket. It was a slip-on, twist to lock, bolt to secure affair. Later the sprocket was held on by a nut and locking washer. In both cases the internal splines are the same so, as in the case of your JT, the manufacturer can make a sprocket, drill and tap it, and it is good for both versions of output shaft. I'm pretty sure you can buy a drilled and tapped 14 tooth and 16 tooth from JT.
...I'm curious if you HAVE to use the clutch hub with the kicker gear, or if I could retain my stock clutch , since I don't really care about the kick-starting.
If it's simply just a case of flopping the 600 gears in my 650, then I'm all over this! ...
I think it is as simple as installing a 600 transmission. You should look to buy as complete a transmission as possible, even though there may be some redundancy. Get the star wheel, the drum, the fingers, the shifter arm/shaft. In other words, the whole shebang, because I can't say that you could get away with just the two shafts and gear sets.
You can use your current clutch.
Here's a bit of a run-down on the clutch basket and primary drive stuff.
The very first clutches, on the 600, had both the hub gear for the kick starter and a lower primary drive ratio gear set. The 650 clutches had a higher primary ratio gear set but retained the hub gear for quite a few years because the kick starter was available as an optional kit.
At about the time that the kick starter kit was discontinued, the hub gear was omitted from the clutch basket. Interestingly, they continued to bore the kick starter shaft hole in the right side case and the inner case and also drilled and tapped the holes for the kick-starter stops inside the case. I don't know if they are doing it to this day, but I know you could install a kick starter at least up to the 2009 model. All you needed was the kick-starter junk, an early clutch basket and an older right side cover with the shaft hole in it. It all retrofit easily. It wouldn't start the engine no matter how hard you kicked it (please don't ask how I know this), but you could install one. Some years back, even though they were doing all the machine work for the kick starter assembly, they quit boring the kick starter shaft hole in the right cover. It's a mystery.
If you want to build a trail bike, put a KLR600 primary gear set in, a KLR600 transmission, and a 14 tooth front sprocket. I guarantee you can take it out to the desert and bury the rear wheel in a heartbeat.
If you were to decide to go with either the kick-starter, the 600 primary, or both, you'd need one of the earliery clutch baskets. Some worry that it had only 7 plates in it rather than the 8 in the later clutches. Not to worry, it's plenty strong and that basic clutch design and those very fibers and steels have been used on bikes making over 100hp. Further, they've gone back to a 7 plate clutch on the latest models. You can break anything by beating the carp out of it, but who like carp?
I'll wager that's more than you needed, let alone wanted, to know.
If you decide to do it, please do a write up here. It would be good to see a current write up of what's involved in making the idea a reality.