If you have the seal out just lay it flat on the left & it'll drain out while ya go have a cuppa. Be sure the oil tank has oil. Take the bleed screw out of the pump & count to 60. Then go start her up. Oh, put a new seal in & mag back on first lol. Love RT1 piston port motors. Ps be very sure to Fully Tighten the magneto nut or timing will wander off along with the crank key. Look forward to some good news soon.

Thanks RT I'll lay it down and let it drain. Looking around on this great site, it looks like the oil flooding can happen when the bike sits for a while. This bike sat for about 20 years it looks like so it's no surprise that it was that flooded.

20 years haha, yep that'd do it. Yamaha unintended way of preserving the old motors for later use.

I just took a closer look at the bearing. There is some rust on the ball cage. 2 spots are pretty rough. I'm debating on if should I tear the motor apart now or put it together the way it is and run it until the end of the season when I have the winter and more time to change them out. I don't think I could do too much damage by running it occasionally the way it is. I really want to see this thing run!Thoughts? 

Come on, start her up. You'll know straight away if it needs dismantling. If it doesn't sound like a concrete mixer it'll be good. Had my AT1 sit for a year. Well it's done that many times but once it was stuck then growly to turn over & didn't make sense why it happened that one time. Started up growly but gave it a very oily mix for a bit & is still "good as" today about 3 years later. Yours won't be good if it's had water in though. Sorry to add that thought.

I'll put it together. If it sounds like a box of rocks I'll have a project for next winter. To be continued...

It's allliiiive!
I finally received the needle jet after waiting a week and a half and having to order another one because the first one got lost in the mail (it still is). It started on the third kick, smoked like crazy until it cleared out the remaining oil in the crankcase. Runs good now. I'm still running on mixed gas until I get the oil pump operation verified. It turns out that the exhaust baffles were cut off, so those have to be replaced (on order from ebay). The main bearings sound good, for now. Hopefully they will stay that way for a while.
Next in line:
1 check oil pump
2 right crank seal
3 front and rear brake shoes
Thanks to all who helped me on this (so far) especially MarkT and RT325!
Dick
 

Congratulations!!!  Well done.
 

Yes, we'll done. Love RT1's.

I just realized that I ordered the the cheap seals for the crank. I didn't know there was that much of a difference! I replaced the left side with the cheap one and will redo that when I do the points and condenser. Haven't got into the right side yet. I ordered the right OEM one on CMSNL I never used them, I hope they are legit. The left one (93103-30044-00) seems to be very hard to find. There is one on ebay for $70 plus shipping! There are a couple for around $10 that have the double spring seal but that seems too cheap and they don't have the teflon or whatever it is on the inside. Not sure which way to go. $70 bucks is alot for a seal but I guess it's supply and demand.