Yes on the thumb pain when changing from a hybrid with flat bars to a road bike with drop bars. It took awhile to adjust but not too long at all. Those muscles seem to adapt quickly. As Trek420 hinted, you should definitely be wearing good cycling gloves if you aren't already; and you want to change hand positions frequently. On top of the hoods is generally the "neutral" position where most cyclists spend, say, 75% of their time, but you also want to use the tops (mostly for climbing or cruising on flats) and drops (mostly for descending and sprinting fast on flats) some too. It can take some getting used to to use the drops, but the more you move your hands, the less pressure any one part will feel. If the pain goes away in a week or two (like mine did), then it's nothing to worry about. If it does not, there might be a bike setup issue, so report back if it doesn't improve.
Good luck, and congratulations on your new bike!
Emi
Emily
2011 Jamis Dakar XC "Toto" - Selle Italia Ldy Gel Flow
2007 Trek Pilot 5.0 WSD "Gloria" - Selle Italia Diva Gel Flow
2004 Bike Friday Petite Pocket Crusoe - Selle Italia Diva Gel Flow