Hit some rough pavement and see how the suspension handles it. You'd be surprised how much of a difference 10-15 psi in the front downtubes makes on preventing bottoming-out. If you're over 200 lb you probably want to try the higher numbers on the rear shocks, the top chrome plate you'll see is numbered 1-4, 1 is least damping, when the # is at the 3 0'clock position if you were on the bike, right-hand shock.
Look at the fork stops on the bottom triple tree to see if they are intact. You can also use some surveyor's line to loop-around the front & rear tires about 6" off the ground, to see if the wheels line-up, w/the handlebars.
Usually an out of alignment handlebar will be very evident when you are riding. It may be nothing more than loosening the bolts in the front end, and re-tightening them in the proper sequence, and torque settings. Sean's video on steering head torque is very helpful. Loose or too-tight steering head bearings causes wandering handling, and possibly shimmies, as you decelerate. Around 40 mph seems to be a point at which people having steering stem tightness issues get headshake.
Look at the downtubes where the oil seals wipe. Any corrosion there will tear-up the fork oil seals, and there's no way to fix that, except new downtubes and seals replacement. Oil in the top of the fork slider is a clue.
If the bike jumps out of 2nd (or any) gear when you accelerate rapidly, look for another bike, unless you're an experienced mechanic and know that you're now facing engine removal, case-splitting, and hundreds of dollars in parts. Shop labor for this repair is probably more than the parts, and I doubt many dealer shops would quote you < $2,000 to do this.