Did you go from no riding at all to doing 30-45 minutes a day/6 days a week? That's a big jump. It takes time to get used to sitting on a bike saddle of any kind, and it's possible you may have to take some time off to let your problems heal completely before getting back into it. And NY Biker is right, a very soft cushy seat will make things worse. You end up "bottoming out" the padding (pardon the pun) and sitting directly on the hard plastic shell, plus of course the padding can create chafing. The more you weigh, the firmer the padding on a saddle needs to be. Some people end up getting leather saddles with no padding at all, but if you're presently in pain, I'd suggest easing into that gradually if you try it. You are probably a bit bruised in places and any saddle at all is going to hurt a bit right now.
As for the hand problems, that isn't uncommon with flat bars, as there is only one hand position and you're sort of stuck with it. One solution might be add-on bar ends that give you one more position. Here's what they look like:
http://oldglorymtb.com/wp-content/up...cip_barend.jpg