This may not be it either, but with my stage one upgrade to air cleaner, Screamin' Eagle II's and then the carb, I had problems at first. I did some reading and the Yost wasn't the top of the list of choices either. I put an '88 sporty needle in and went up to a 48 pilot jet. This almost did the trick, but it still acted lean when cold and restarting. Several articles mentioned that the stock main jets were fine for stage one.
Checked into a 50 jet, but a Harley mechanic said those were only used for racing and such hotter engines, so I removed the pilot and put a sewing machine needle in my vise and pushed the jet down sideways on it, thru the vacuum holes, and peening them out a little.
Hanged if that didn't work! It still requires the enrichener open at first, but not for long before it runs perfect, even at altitude. Oh, and I get about 38mpg at sea level, and up to 46 in the mountains.
I'd say the Yost tube may be at fault if your seals are good, but check them first.

 

Man I already replaced the gasket where the carb meets the manifold. Unless it's leaking where the y manifold meets the heads. Where else could it be leaking. I previously capped the pet *** vacuum hose for the old school type pet com.

 

Thing is I put the host tube because I started having this problem with the stock configuration. When I did the stage one I did notice a harder start when cold but not like this. Now I can't even hold steady high rpm throttle without having to gun it over and over. It coughs and spits for about 5 to10 minutes then runs perfect. I'm lost. Maybe it is my manifold seals. It makes sense that it is running way lean til warming up. Somebody must of had this problem before.??????????

 

Gawd, that would drive me crazy. OK, we're assuming there is no crap in the carb, the piston is moving up and down freely when cold, and the accelerator pump is pumping cold.
If all that works as should, that leaves the choke enrichener failing you or back to the pilot jet as far as I can guess. I wonder what number you're using, but if it straightens out while still cold, that ain't it.

 

48 slow jet. Jost needle set on 2nd slot. Running porker pipes with drilled out baffles. Stage one air cleaner with filter exposed. Also when I pull my choke **** out all the way the rpm's go up to like 3000. Or to put it simpler the bike reves up dramatically. Still though, problem started before I ran this set up. And it runs like a champ once it warms up.

 

Now, with that in mind, it's probably not the Yost tube. It sounds like the enrichener circuit isn't functioning properly. Sounds like you're getting a lot of high idle bump, but no rich mixture. My idle comes up, but not super dramatically, and my exhaust definitely has a rich sound with that odd chugging of a choke mix. Not so rich that I see black smoke though.

 

Man I replaced the choke cable last year, but just the cable and did not check the inner workings of it. I'm going to dissasemble it today. Although I'm not sure how the inside of it could malfunction. I really need to buy me the maintenance manual, I have been putting it off for some time now.

 

How many turns out is the idle mixture screw? Has the plug been removed so its adjustable

 

My 02 FXD needed a 50 pilot during the winter months

Bad Idea, the little holes in the side of the pilotjet are air bleeds, making them larger makes the mixture leaner

 

I thought they were suction holes. Oddly, it seemed to help. And I am thinking of a 50 for the winter too, as she still pops and coughs in the cold mornings. I may end up leaving it in there; sometimes she pops on hot days too, but I think that just may be because it's a carb.
Now I done posted everything I think I know about CV's! Learning time now.