Have you actually ever tried to ride the darn thing? 

Or at least do more than start and rev a few seconds? 

It sounds really loaded up.  You might just need to ride it. 

Hopefully MarkT is right I remember my grandmother asking me to go blow the soot out of her 64 Falcon of course I said YES 

If i go back to the video on page 5 it clears up just before the video ends so i assume you turned the fuel off & carb was running dry [think you mighta said that].
So back to the exhaust. Take it off & put ya ear muffs on then give it a rev.
As it cleans up in page 5 in the last two seconds it proves spark is regular [in my opinion].
I can rubbish my exhaust theory though because, if it was severely restricted i still think it would be clean at idle--but it isn't--& every time you shut throttle & bring it up slightly it's still super rich right from the start.
Are you sure its got a pilot jet in the hole?, or not just a short pilot out of a smaller carb.
No jet would leave a quite big hole with two outlets, straight up & compensating hole on an angle--actualy i think its the other way around but!!.
I know the answer. Petrol station filled the oil tank with fuel & it's pumping it in. Ok not that.

We've not seen much sun for a few months over winter & yay it's shining today so thought i'd start the DT1 because it's been sitting for those few months pretty much, stale fuel & all.
Also mainly to show on this post [my mechanical ineptitude haha] of clearing its throat.
Motor sounds lazy because it has a brass overlay on the flywheel, umm, & a 360 carb, & a short skirt DT1MX single ring piston, but heavy flywheel lazy.
Trawling my memory as probably been 25 years since been inside it.
Anyhoo--just demo-ing to show what i think OP BHEPP15 should clear like--if it was going to clear, which i don't think it will.
Vid has 1080 quality availeable by the looks, not that it affects the sound as far as i know. Set the cellphone on a trypod with rubber bands & looks like it was pointing about perfect considering i couldn't see where it was pointing.

Someone once trucked their bike to my house to let me look at it after a "rebuild".  (Engine was not actually taken apart, the definition of "rebuild" apparently varies)  He had been starting it in the garage for brief periods.  It sounded rich and missed like heck when you revved it.  I asked if he ever rode it and he said no.  I told him to jump on it and take it around the block (which was almost two miles where I was living at the time).  He came back several minutes later and it was running fine.  It just needed to be warmed up and ridden with a load on it.  Which is why I suggested it, that last video of "full throttle" was only a couple of seconds that repeats endlessly. 

Someone could have drilled out jets or something...  I've seen that, even the needle jet drilled!   And of course there are those "carb kits" that have parts stamped with stock sizes but are not the same.    I don't remember if it was verified if this carb has genuine Mikuni brass and slide needle but I think it was.  Using a main in bottom of needle jet bypasses the whole o-ring and it should have run reasonably well if o-ring seal was a problem. 

It still could be ignition.  New condenser could be crap or something.  Here is my old video of a CDI stator acting up...  They all had great spark and started easily.  Same CDI box used.  The first example would not rev much above idle.  You can hear the "baaaaaah" when the throttle is opened.  It just chugs like it's very rich or loaded up bad.  It's not.  The second stator does rev a little but is erratic.  It will not rev out.  Finally the original stator for the bike revs fine.  

Source coil and pickup coil resistance readings were all in spec. 

I checked all of these with an old SnapOn scope I have with bike running and I could not really identify the problem.  That probably why Yamaha had some basic CDI checks and then said "replace with known good" as a troubleshooting step. 

With all the carb work you've done it might be worth swapping ignitions.



 

I have tried to ride it, although it didn’t get me far. Doesn’t like to ride and that day it really wasn’t revving although this weekend I will try and ride it again before I do any other changes. 

RT that sound brought a smile to me, hopefully I can hear that for myself soon. might as well try taking the exhaust off as a try too haha I’ve got some ear plugs in the garage. 

yes MarkT I think that if it doesn’t clear up with me running/riding it this weekend I will swap my rt3 ignition in and see if that does the trick. I know that my rt3 revved before I tore it down so that will narrow it down for me. The only reason I haven’t yet is that since I relocated the condenser I soldered it in instead of using crimp connection so I haven’t felt like undoing that although it really isn’t hard. 

HT1, I take the head off have my dial gague mounted above the center of the piston. Use a battery and a timing light. Turn the flywheel back and when the light dims it should read 3.2mm BTDC. Tighten up the points and then check to make sure they didn’t move. Then re assemble. 

I have a spare dt3 carb yes. It is not complete though. I actually have a spare dt3 engine that was torn down and given to me in a box but there is a lot missing, like the ignition and flywheel. 

Just for kicks, turn the fuel off & let it run dry but see how it revs for the last gasp but in the same breath turn the fuel on & catch it while at clean revs & lets listen to it drown out--just to be sure to be sure.
I my opinion--the fact that it revs clean before the video ends wipes the spark theory, just saying.
But i get very one eyed at times & can't see the wood for the trees so might be wrong.

Clockwise? I know it gets frustrating but you will be a pro when it is solved these kind of problems can make your head spin

Clockwise yes, very frustrating. I can’t help but keep thinking maybe it just needs a top end haha that’s too simple though.