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I got my JIS Impact Screwdrivers from John @ Economy Cycle. 

https://www.economycycle.com/product/vessel-jis-crosshead-impact-type-screwdriver-set-23/

Super nice

   You can leave that bushing in.  It shouldn't vibrate out since it is pressed in.  I left it in place in my race motor.  You can try to give it a tap from the backside and see if it budges, then pry it out.  OR just run a loop of safety wire through the center of it as insurance.

The fork lowers and front hub are desirable for a dual disc front end.  If you are so inclined

   Also, when putting the carbs back together after cleaning, note that the bowls are 99% identical, and can be interchanged by accident.  The bowl that goes with the left carb that has the brass tube will have a little hole at the bottom of the chamber that the tube inserts into.  That little hole feeds the fuel to the choke (enriching) circuit.
   Easy to swap bowls by accident and then the bike is hard to start after cleaning/rebuilding the carbs, because the choke is not getting fuel.

NOT MINE! No idea who the seller is.  But if someone makes a deal, I could pick it up and store it Inside for a couple of months until the buyer could make arrangements to come get it. In DeLand FL.   

https://www.facebook.com/marketplace/item/720615890342835/?ref=browse_tab&referral_code=marketplace_top_picks&referral_story_type=top_picks

Very nice.  Also love that Yamaha still offers a lot of replacement hardware for 50+ year old models.

Blue ScotchBrite pad and Barkeepers Friend

I am usually removing/refreshing a Mop-N-Glo finish when I do this.

Blue ScotchBrite pad and Barkeepers Friend

   And after getting the M/C sorted, Don't NOT rebuild the caliper as well.  Brakes are a 'system', not just a collection of parts, and spending time/money at one end and not the other is not the best choice.   

[IF]

can you drill and tap the other side of the carb?

That^^^  IF the slide is machined on both sides for an idle screw.  I am not familiar enough with the TM slides.
How often do you need to adjust the idle?

If you just want it to breath better, and make more noise, you can probably go this route for a lot less $$:

https://www.ebay.com/itm/186254427616?chn=ps&mkevt=1&mkcid=28&google_free_listing_action=view_item&gQT=2

  On My WR250R I left the stock exhaust, because for me it is loud enough, and the 1-2HP gains from spending $600 on an exhaust system seems foolish    I did spend about $1000 on the suspension.  As far as fueling mods, I did remove the AIS, did some air box mods and added a K&N. And added the EJK, just to make sure it still ran smoothly, not really in search of power.
   I understood, when I bought the Yamaha, that I bought a motorcycle that makes less than 30HP, and I am fine with it.  If I wanted more HP I would have bought a Beta 390 or 500.   

(I do understand that the AIS has nothing to do with fuel settings, as it is down stream of the combustion chamber.)

   I have the EJK on my WR250R.  Works fine.  You can go with the recommended settings, for your application and mods, from EJK, and then tweak if you feel the need.  There is plenty of info on the Kawasaki forum regarding the KLX/EJK regarding different set-ups and settings.

You can leave all the parts out; from the shaft to the cable drive.  Then I use one of these.  Caps off part #10.
 
https://www.mikesxs.net/yamaha-xs650-tach-drive-block-off-cap.html

  If it is a 350 6-speed, all the R5 clutch bits and countershaft sprocket will swap over.  If it is a 400 6-speed, you will need a 400 (or Banshee) inner clutch hub and a 400 pressure plate and springs/bolts, as well as a switch to a 400 c/s sprocket.  The R5 clutch and basket should be fine if you have a 350 6-speed and are sticking with the R5 clutch assy.  However you may need a bit of 'three-card-monty' with the fiber and steel plates to get the correct pressure and friction if switching to a mix of later 350 or 400 bits with the R5 basket.
   The 6-spline drive end (clutch side) is 400. The output shaft also has a 6-spline output c/s end.

I have this one. It works fine for hauling my dirt bikes. The heaviest I've ever had on there is a touch over 300 pounds. I've had it for several years, and I used it just the other day.  The 400# version works fine for me.

https://www.harborfreight.com/400-lb-capacity-receiver-mount-aluminum-motorcycle-carrier-62837.html