thanks for the comments and ideas everyone it helps A Lot!!

, I finally made some progress on this thing!

I put the tires to 30 PSI like RT said and that helps 50%, that made me think to make the steering lighter and I did some google searching and read weaving is caused by the steering head too tight. I had previously adjusted the steering head by feel so that the steering barely flopped over on its own. this time I loosened everything, and then use my torque wrench to torque it to 30 ft lb to seat it and then I loosened it and torqued it to 18 ft lb. now the steering feels lighter and the bike goes perfectly straight at low speed but the high speed wobble is back, I think I just need to spend some time fine-tuning this preload on the headset!!!

Try balancing the front wheel. Or both wheels. Out of ideas myself.

Is it a weave or a wobble? High speed weaves are often down to swing arm flexing.
The handlebars will feel like you are rowing a boat.

Coming in late to this discussion but a lot of really great suggestions for anyone during rebuild/maintenance. I really like tinkicker's post on checking rake and castor, will have to try it on mine (although it does not exhibit the weird behavior at all).

I see you did add the needle bearings for a XS650/RD350, as a general FYI the bronze swingarm bushings meant for an RD350 will also fit the '74 swingarm just fine. Should also work for the 250 and '75/'76 larger models as well.

I know that the swingarm bearings are new... just wondering if swingarm has any end play in the frame that needs to be shimmed out or play in the bearings... not really the bearings... but for example the swingarm bolt should be a close fit in the inner sleeve and the inner sleeve generally needs to be securely "pinched" between the frame tabs. If you couldn't tighten the swingarm bolt to spec (~80 ft-lb) without the arm binding up, the problem might be in the pivot?

Also, make sure rear axle is tight. (~86 ft-lb). I rode a squirrelly 400 once and the rear axle would shift around because it wasn't tight enough.

Oh, the above issues with the swingarm pivot shifting and the rear wheel shifting did NOT show up pushing on them by hand.

Everything seemed tight. But under the force of driving parts could shift.

Sleeve I'm talking about that needs to be pinched tight in the frame is to the left in photo here: www.mikesxs.net/yamaha-xs650-swing-arm-needle-bearing-kit.html

Shims may be needed to center arm on sleeve and only have a tiny bit of end play.

I know exactly what you mean about the swingarm endplay, I had to add an additional shim than what came with the kit in order to get it to perfect clearance, its nice and tight with no side to side movement, but no binding, its smooth. I used my depth gauge to measure .5mm of endplay from the sleeve. I tightened the swingrm pivot with a breaker bar but I could check the torque, I also have checked the balance of my front wheel and its good, some weights are on it. I didnt check the rear balance yet.

I was initially haveing problems with a "weave" at low speed, it doesnt oscillate, it just doesnt want straight lines.
Loosening the headset to 18ftlbs and more tire pressure results in perfect low speed handling, but a high speed "wobble", a slow oscillation like rowing a boat, that could possibly progress into a tankslapper.
Only under hard acceleration over rougher roads above 55mph.
I think if I find the sweet spot of bearing preload and tire pressure I can sort it? I will report back my findings.

Are both your rear dampers actually damping?

Headstock torque fixed it?

cliff

If the frame isn't bent and the wheels are inline, swap the front end and rear shocks, from the bike that handles onto the one that doesn't.