Hi Guys, Im looking for some advice on I assume my issue to be suspension related.
I have been slowly working through issues with this bike thanks to forum members and most issues have been resolved.
My next issue to sort is vibration of sorts, when im riding the bike at slow speeds up to 30 mph its a little bouncy (feel the bumps) but after this at say 40+ my eyeballs and glasses are shacking to the point its dangerous as cannot see properly.
fI I lift my butt off the seat then all feels good on the eyes and comfortable.
the bike has new tyres fitted before I got it, also it has aftermarket shocks fitted. the adjustment on these gas shocks are the spinny nut arrangement at the top. I have adjusted these to full soft (hardly any pre load as I thought this was the issue, too hard) but the rear end still only moves a little if you bounce on the bike (previous owner 17 stone, im 11 stone)
So Im assuming the issue is coming from the shocks (cheap ebay ones) and not the forks? seat foam is soft.
There does not seem to be any bouncing from the front end, taking corners on the bike seems like you have to force it in the corner and it wants to ride wide    Hi Guys, Im looking for some advice on I assume my issue to be suspension related.
I have been slowly working through issues with this bike thanks to forum members and most issues have been resolved.
My next issue to sort is vibration of sorts, when im riding the bike at slow speeds up to 30 mph its a little bouncy (feel the bumps) but after this at say 40+ my eyeballs and glasses are shacking to the point its dangerous as cannot see properly.
fI I lift my butt off the seat then all feels good on the eyes and comfortable.
the bike has new tyres fitted before I got it, also it has aftermarket shocks fitted. the adjustment on these gas shocks are the spinny nut arrangement at the top. I have adjusted these to full soft (hardly any pre load as I thought this was the issue, too hard) but the rear end still only moves a little if you bounce on the bike (previous owner 17 stone, im 11 stone)
So Im assuming the issue is coming from the shocks (cheap ebay ones) and not the forks? seat foam is soft.
There does not seem to be any bouncing from the front end, taking corners on the bike seems like you have to force it in the corner and it wants to ride wide    
I have the original therma shocks that I intend to do a light restore on them as per the excellent guide in the files section to see if the ride is any different  
I have the original therma shocks that I intend to do a light restore on them as per the excellent guide in the files section to see if the ride is any different 

First.  Eyeball the rear tyre to see if the bead is fitted concentric to the rim.  It may be that a portion of the tyre has not spread out into the sides of the rim and is running in the centre well.

Second.  Lift the rear wheel from the ground on a stand and put a marker near the rear wheel.  See if the tyre centre  tread approaches and moves away from the marker when you spin it.  I have seen misshapen tyres in the past cause similar symptoms to yours.

 Third.  Using the marker, check to see the rim is concentric to the hub.  IIRC yam service limit for concentricity  was 2mm.

Fourth.  Remove the chain, back off the brake and check for a severely out of balance wheel.  

Tires and rims out of true or balance. Possibly bent sprocket. Even if wheels spin true could be out of balance. Different view points from members here but good idea to have balanced. I bought both stick on type and the ones that fasten to spokes. Hopefully not a bent output shaft. Good luck.

I would add do a visual check on the front shocks. Put it up against something solid and see how they compress with and without heavy pressure. If they take effort to compress It could still be the fronts. I had the same issue and turn out the fronts were bone dry and gunked up inside. They still compressed but with quite a bit of effort. I felt all the bounce in the rear. 

Balance the wheels.  Make sure the brakes are totally backed off and remove the chain and spin the wheels making sure they are totally freewheeling.  Get some lead weights from a tire shop and balance the wheel as good as you can using gravity then if you have a air gun get the wheels spinning as fast as you want and see what happens at a higher speed.  I've done this many times and you should be able to get these wheels balanced enough that it wont be too noticeable at the speeds these bike can go
Doug

All the previous points are good, what tyre pressures are you running?
I had my RT1 wheels balanced as the rimlocks make quite a difference on the road at speed.
Also, does the swing arm move freely, might need to remove the shocks to check.
 

My money is on Tinkickers first suggestion.
I had the same issue once and that's how it panned out for me.

I agree with Tinkicker, Pedalcrazy and Schu.

When you say “taking corners on the bike seems like you have to force it in the corner and it wants to ride wide” you should check your steering head bearings.  They can get notchy and contribute to handling issues.  Often there is a notch in the straight forward position and the bike wants to go straight.  Prop the front wheel off the ground and make sure you can steer side to side smoothly.

Also, you might want to check front and rear wheel bearings.  If they have side play they can amplify the out of roundness feeling you get from the tires and rims.

Loose swingarm bushings can also contribute to handling woes.

Good luck!

I have a different take, as I think I understand what you're saying about your eyesight during the vibration. I had this same effect on my 1971 DT1, at certain speeds, but it was not necessarily "speed," more the load on the engine, at the RPM the engine was at, at the speed I was going. For me the eyesight effect was annoying more than unsafe...but I think I know what you mean.

I replaced the entire seat, and 2 missing rubber bumpers on the new pan (used one of KDI's offerings, new pan/foam/cover). The old pan was cracked, and foam completely flattened, and yes 2 missing bumpers. Was surprised to find that the vibration causing my eyesight issue was completely gone! And has never returned, some 600 miles later.

So...I think your seat pan is directly contacting the frame, transferring "normal engine vibration" into the seat pan, and your body. Me, I'd look to see if any of the frame-to-seat pan bumpers are missing, and look for seat pan contact points to the frame or any other solidly mounted component under the seat. 

After that, I would check for loose engine mount bolts, or cracks in engine mounting frame lugs.

The only time (so far!) that I've experienced anything like this was years ago, when the owner of my local garage let me have a go on a speedway bike up a local lane - I was/am such a wuss that I only rode it at low revs and ended up not really being able to see where I was going!