Cables work smoother when set in a nice curve as you have, but there's a danger the throttle cable could get squashed in the steering stop so just be very aware of that.
But thats irrelevant to the slide issue. With carb bolted to the motor & no cable can you get your finger in there & push the slide up then let it drop under spring pressure'
Assuming that's all good then are the cables fully home in the junction box because that's a common trick to catch people out.
Cables can't realy get crossed in the junction box like they can on a twin cylinder if assembled wrong but the outer has to be fully in for both bottom cable & top cable.
Back off the twist grip adjuster fully so the junction box slide goes right back.
Back off the carb top adjuster.
Be sure the cable is seated in the slide.
Give it a full throttle hard wind open to pull everyyhing right home.
Ok, not any of that then i guess must be as others say--wrong cable.
So it'll be the lower throttle ya worrying about & many times with wrong cables i just force the ferrule off then 'carefully' get hold of the end of the outer & un wind it some then cut it hopefully without snipping the inner wire.
Alternatively i just unsolder the lower nipple & cut of what you need of the outer then resolder. Nipple will probably need heating then bit of compressed air to clean the solder out fully--or drill.
Something like that. Done it many times. With the ferrule i just tap the back of a drill in to open out the couple of center pop marks so it'll go back on the outer good.
ps, if you do the nipple solder thing it always ends up too much solder so just remember that or it won't seat in the slide, or might not even fit through the adjuster.

This may sound like a a Crazy idea but what position is your autolube cable at when stuck at half throttle ? How does it operate 

i.imgur.com/31UWLn5.png 
   This throttle tube gives you more slack

i.imgur.com/xBZcO1w.jpeg
 This tube gives you less slack

  I’ve had a similar problem before with to much slack

Gr8uncleal, the cables came from KDI Repros (214-26311-02-00 and 214-26312-00-00) and the connecting tube (214-26261-00-00) came from my Yamaha dealer.

MarkT, when I just yesterday took everything apart, I checked each component along the way and all operated properly.

RT325, with no cable, the throttle valve (slide) goes up and down smoothly within the carb.

Ht1kid, the autolube cable functions properly (and it, like all my cables, are new from KDI Repros).

Now, for an update: I put everything back together. The only thing I haven't done is put the foam with black tape back on and I haven't put the tank back on. I gave the throttle some twists and the throttle valve goes all the way up and all the way down like it should. (I made a little 33 second video of this, but it just shows what I'm describing here.) The only thing I can think is maybe the black tape from the foam was holding the throttle cable to the frame, and this prevented something from functioning right? I don't know. When I do put the foam and tape back on, I will make sure nothing is trapped or binding anywhere.

Long time no post. Tank and seat are back on. Push-started it this morning with success! No stuck at high revs, nice and normal when using the throttle. Adjusted the throttle cable at the grip to get the RPMs down a bit. Am attaching a video so you guys can hear the engine. I hear something that sounds like a buzzing or rattling. Is this normal?

Idling,
flic.kr/p/2qm1RKL

Turned key off. Kick-started immediately with one kick. Turned key off, waited 10 minutes, kick-started - one kick. Waited about 30 minutes, won't kick-start at all. Oh, well. One problem at a time.

Long time no post. Tank and seat are back on. Push-started it this morning with success! No stuck at high revs, nice and normal when using the throttle. Adjusted the throttle cable at the grip to get the RPMs down a bit. Am attaching a video so you guys can hear the engine. I hear something that sounds like a buzzing or rattling. Is this normal?

Idling,
flic.kr/p/2qm1RKL

Turned key off. Kick-started immediately with one kick. Turned key off, waited 10 minutes, kick-started - one kick. Waited about 30 minutes, won't kick-start at all. Oh, well. One problem at a time.

I hear something that sounds like a buzzing or rattling. Is this normal?

I'm not the person to ask about sounds on videos, camera microphones sometimes pick up and amplify sound you really can't hear at all in person. 

That said, I didn't hear anything in the video that made me think "that's not good" or that sounded terribly abnormal. (Usually if someone posts a video and doesn't even ask about a funny sound, several people will say something if they hear a concerning noise)

Make sure you're shutting off the petcock when you shut off the engine.  If float valve is seeping, and many do even back when these bikes were new, the engine can flood when parked with petcock on for a while. 

Yes and mine does that.

Thanks, shyted. Thanks, Mark. I do always shut off the petcock when not in use.