Sounds like a mechanic that I too would trust! -
What you can do is to check that the tires are set properly on the rims - there is a marking/line that goes around the tire. It should be at an even distance to the rim - if not => bad vibbrations.
Then check the rim - just lock the frontwheel (straps crossing over the tank to either side frame will be good enough). Put something next to the rim that will allow you to see if the tip of a screwdriver (or similare; pen, stick, whatever) follows the rim at the same position all around; and if the rim is skeved or straight.
To do the same with the rearwheel - you need to weigh down the front end; here an assistant will be handy to have.
If these two simple tests pass - you can be fairly sure that the wheels are ok.
It is very rare to have wheelbearing problems causing bad vibrations; but it can happen. Spinning the wheels installed wont do it, but will give you an idea of if something may be amiss. When did you change the seals and regrease the wheelbearings last ?
When you turn the rear wheel back and forth - any noice, rattling, spocket "chewing" ? How does each part of the transmission sound (large screwdriver pressed against the tragus (ear) and against the site on the bike where you want to focus the listening) ? The bevelbox should be "silent" and the shaft should only have a sound of the joints "snapping" over. Any suspisious sounds from the bevelbox may indicate worn bearings or too worn splines.
As for the gearbox... Oak Oshlen wrote about it in ABC Newletter back in early 1990:ties. Best way to test is to secure that the rearwheel is spinning freely in the air = strap down the front-end.
Start the engine, let it run at 3000rpm and put it in 1st - moving up to 5th and tehn back down to first and neutral. If there is a bad bearing in the gearbox you will hear it! Sounds like the rumbling sound of the machines at quarries grinding rocks. If uncertain - use the large screwdriver again; a bad bearing will jolt you backwards. Thats how bad it sounds.
Loosen the gaiter/bellow on the shaft at the gearbox. You need a 10mm wrench(?) - just feel that the four (4) screws/bolts securing the shaft to the gearbox are tightly set (put the gearbox in 1st - you will not be able to stop the shafts movement by holding the rear wheel). These bolts are stretch bolts and shoudl be renewed everytime the shaft has been removed... I have opted to use wave(?)-washers instead - never had any bolt gotten loose since then. If you want to play it safe - see to that you have a set of new bolts and change to them; to set the correct torque is awkward due to the limited amount of space; I simply use a short 10mm wrench (10cm or so) that will not give me too leaverage.
The swing bearings should be regreased at least once a year - using a greasegun. If they have not been regrease for some time... you need to take off the swingarm and pull the bearings.. this will damage the seals and you will find it easier to buy new bearings... fill the hole with grease (some swingarms lack the steel lid in the bottom of the left side - make one and install it.
Also check the stearing bearings, steering damoer, and attachments of the rear shocks. When did you last overhaul the rear shocks and forks ?
Rear chocks shoudl be overhauled every 3 years or 30-50 000km. Forks should have new oil at least once a year ( I use Omega 699 automatic gearoil 5W/20 = same damping cold as warm => more predictable tracking and better damping). When did you last pull the springs from the forks and measure that they do hav ethe same length ? If you could you should also check that they have the same strenght. There tend to loose power and lenght over time... and can cause a wobbling tendency as well as vibbrations...
Check that the rear frame is securely bolted to the main-frame - never seen one to be loose, but it could happen.
Is the enginebolts/rods/axels tightly pulled ? I did check mine - still as I mentioned they became loose...
What you can not check so easilly is the clutch. If the clutch has been impropperly assembled you may encounted vibbrations like you describe - never seen it, but heard lots of reports on it and claims by owners that they have suffered it. This is... how can it be incorrectly installed ?... I've tested to deliberatly not reinstall the clutch with the old markings and have not experience any extra vibbrations... I know I could be lucky.
Remeber that the clutch is supposed to be balaned and if reassembled one position off could result in unbalances causing vibrations.
A worn clutch-plate can cauese vibrations.
Looking forward to your road report and hoping dearly that you will discover the vibrations to be speed related and not rpm related.