First off, I'm very excited by the power of this thing!  That was not the case yesterday.  Yesterday it was still cutting out completely on hard acceleration.  I was planning to ask you experts for help but decided to have another go at the carb so I could report what all I had tried first.  I discovered a small problem.  The main jet and its washer were sitting in the bottom of the float bowl.  Today it runs perfectly!  I think it's remarkable how well it ran with no main jet.  I can't exactly picture what was going on but I assume it was getting extremely flooded with a hard twist.

Now I do have one remaining issue that I'd love to hear ideas on.  Before I restored it, it had sat for 30 years and it wouldn't shift.  It was suggested that I check the cam stopper.  That was the culprit as the stopper was firmly rooted in the retaining plug with the spring fully compressed.  Freeing the stopper restored the ability to move through the gears.  It runs well now but still has trouble downshifting.  It will almost always shift down one gear easily but in order to go down any lower, I have to lift up slightly on the shift lever and then step down for the slight click down to the next gear.  Thinking maybe the cam stopper spring was out of spec, I replaced it but it didn't help.  So far that's all I know to try without just flying blind into parts unknown.

Has anyone had a similar experience with a satisfactory conclusion?  The best I can guess is that a spring or a notch in something is worn or something isn't tightened correctly.  Any help would be greatly appreciated.

Thanks, 
Mike  

Great update!  Congratulations!

My first thought on the shifting is maybe something is just "gummed up"...  assuming shift lever isn't rubbing on the case or something.

I'd ride it and see if it frees up...  I don't recommend ATF in these transmissions but it does clean things well.  I might be tempted to run ATF in the trans for maybe 50 miles to see if shifting gets better.  Then I'd go back to the correct oil and change it a couple times fairly soon after the ATF use.

No11 can be adjusted to get what you're hoping to achieve. But if you go in there first just check the lever return spring hasn't been damaged or bent in such a way that it's ears aren't parallel so they touch both this small eccentric screw & the non adjustable stop screw as it slide up past both. That fault will be obvious to feel on the gear lever by having a little play before touching the spring. Have also seen the spring fitted still crossed which wll be easy to see. Never seen a detent plunger stuck down so thats a new one for me & one moreto remember. Also everything MarkT said too. Good that you found the main jet out. All learrning curves those & something you'll probably never come accross again although never forget either.
www.partzilla.com/catalog/yamaha/motorcy...fter-2-250b-c-400b-c

I know the earlier design motors have adjustments on both stop & centralising screws but not the later design!!. 

Mark  and RT325,  

Thanks for the replies.  Mark, you had mentioned just running it a bit first in a response to an earlier post.  Since I hadn't 100% worked out the kinks in the motor yet, I haven't had a chance to put many miles on it yet.  I will definitely do that before I open anything up.  I did change the transmission oil (I'm using Lucas Oil 10W40 for wet clutches) once so far and it did have quite a bit of discoloration and some fine garbage in it.  I didnt' see any metal but it was definitely gummed up so I'll try the ATF for one more flush and put a few miles on.  Today, it already seems to be downshifing better, or else I'm starting to understand its nuances better.  Just now, it downshifted pretty well but I'm still levering up with the toe of my boot just maybe a couple of millemeters before pressing down.  I'm used to my Triumph 650-TR6C which has a pretty robust shifting action.  The Yamaha seems just a bit more delicate.

RT, thanks for the great post and insight into the bits and pieces.  I'm still hopeful that I won't have to get in there too deep yet but with your help, I'm not afraid to try and I'm hopeful that I'll slowly begin to understand how the parts work.  So far it's still a bit mysterious, especially in the shifting mechanism and transmission.

Cheers,
Mike

In the course of the oil changes you are planning ,
it might be worth dropping out the Detent spring again .
As It sits at the bottom of the gearcase , where sludge tends to
accumulate , it may have a fresh load of gunk settling in again .