Check out p.104 in Lee Parks's book Total Control, where he addressed clutch/brake lever ergonomics....rotating the levers down may help.
Try to position your hands and arms so there is minimal/no angle across the back of your hand/wrist while riding - that is, the back of your hand, wrist, and forearm is one "flat" or straight surface. Your wrists should not be lower than the back of your hand.
Also,the stock bar angle isn't for everyone - I found that a Spiegler aluminum superbike bar (a bit more swept back) fit me better and has cured the sore wrists... but 30 mins seems too short a time to cause wrist/thumb pain (if you had said 350 miles....I would agree on needing different positioned bars).
Finally, try resting your left forearm and elbow on the tank during long rides. Work on ab and back exercises (i.e., core), and avoid taking a death grip on the handles....
Good call on the Lee Parks book. In general it's a good read, but that section details some control set up issues.
Also +1 for the core strength work. Additionally, more weight through your legs into the pegs and gripping the tank can help with posture issues and take weight away from you arms.
Many times wrist pain is a result fo too much pressure on the bars. One trick you can practice is 'chicken wings' Basically no matter what your position on the bike you should have some bend in your arms, and there should not be so much weight one your arms that you cannot approximate flapping your 'wings'. IF you try to flap, and you find your arms won't move, then you're too heavy on the bars.
By raising your seat, you are changing your weight bias forward - so you'll need to compensate for that in some way to fix your issue. The free way has already been discussed (core, posture and position). The $ way is higher bars/risers or similar fiddling.
30 min is way to short...