JA-  Taking a step back...  What exactly do you mean by "rich on the bottom"? 

I'm asking because carb tuning is 100% about how far the throttle is open, not what RPM the engine is running.  So if the engine is rich at lower revs but the throttle is wide open or even halfway open, you won't fix it with the pilot jet as the carb is on the main circuit at full throttle and the midrange circuit at half throttle. 

Also, don't discount needle jet wear.  You can't always see the wear in the needle jet. 

One other remote possibility is the condition of the starter (choke) plunger.  If it leaks, it could provide extra fuel under some circumstances...  and no, it won't richen the mixture the same everywhere. 

Ignition timing and ignition system can also do so weird stuff.  Timing is easy to check/set/verify with a timing light and Yamaha had the wrong spec in 78 manual.  It was also perhaps their earliest attempt at an electronic "advance and retard curve" and it's not unheard of for electronics to act up.   I had a friend with a motoplat or SEM ignition that apparently had a weak spark at lower RPM...  it sounded rich as hell (literally four stroking) at low rpm and could not "jet it" away.  And if you tried, then it was too lean at high rpm.  I helped him install a VAPE ignition as a last ditch effort and the problem went away.  (We did notice the timing light seemed to be skipping or erratic at low rpm)

Hope you figure it out soon...  video of what it's doing might be very helpful too...  we're all flying blind here and can't see and hear what you can.

Not doubting your tuning ability & love posts like yours to following how you get it sorted. I'll go back & read MarkT's long post tonight as value his advice on just about everything--ok--everything-- but would reducing the air jet richen the needle due to less airflow rather than lean it out--just curious?. I started mx in about "62 but now mostly race my rocking chair haha. Had all the big bores up to yz490k. Just realized yours is a 250 which was a perfect model in "78 with alloy arm. Just looked right!!. Cheers from NZ.

Sorry, one more-- is it deffinitely rich or just go through a flat area then come on strong. I bought an it400 motor for a project that someone had ported to give close to 200 degrees exhaust duration & the pipe I adapted to fit was  bit short in the mid section. The power came on like a 125 on steroids & was unrideable in the dirt. So added 4 inches to the header as easiest to do in my case. This made it manageable & spread the power out overall.

With the "primary choke" needle jet that most of these two strokes have, the air that goes through the passage provides a "vacuum effect" that pulls fuel from the float bowl.

Take carb off bike, slide out, liquid in float bowl (or bottom of needle jet in liquid).  Use an air nozzle to blow into the air jet passage.  Liquid in float bowl will be sucked up through needle jet and the bowl will empty pretty quick. 

Very dangerous to try with gas as you'll spray gas mist out of the top of needle jet. 

Somewhere I have a Mikuni book that has a chart showing how air jet affects full throttle...  bigger air jet richens mixture at full throttle slightly as RPM (and air flow) increases.  Effect is greatest at full throttle and high RPM.  Really doesn't do anything below 3/4 throttle.  It's a way to "fine tune" the main circuit... and I mean "fine tune".  Makes very little difference so usually not touched except perhaps by the engineers and tuners at the factory. 

It certainly won't fix idle circuit richness if that's what's going on here.

First i can not even post a photo for some reason.lwt alone a video...haha..
Deffinately to rich off bottom at lower rpms and that is why I was leaning toward something done wrong just like the two pilot air screws in carb...one in pilot air screw location and one to adjust idle, haha....
The stator ignition wires wore through insulation and had contacted wires, stangely bike still ran....had 2 socket head bolts heads for main cases popped off so when pressure checking crankcase i had air leak from breather, luckily new bolts cured it..
Will add more info soon as I did get new jet needle but after measuring it i am not sure it will help much..
I did set timing....i can tell you if anyone has owned one of these it kicks back really hard at times, very surprised it did it so retarded timing to 1.8 and it is better...just wish I didn't sell all my jets years ago ....SOB!

Hi Giys..
The 6f15 jet needle ( on 1 position, clip top) and pilot air scrrw at 1 3/4T out did it, Bike rips now..
I have read the 250E is like a 125 and can attest to that...
Thanks for help guys...If i make a video i will post...