Good job, dude, I am impressed that someone of your size and (in)experience actually rode up the hill! Many would have had to walk or give up.
"Good seat", schmood schmeat. Seats are possibly the most subjective component of a bike. Just because it's good quality doesn't mean it's a good fit for you. That said, you kind of have to learn about your anatomy and how to sit. You need to get used to feeling your sitbones (protruberances from your pelvis) resting on the meat of the saddle. Not the nose (pressure between the sitbones on soft tissue! Yikes!), not the 'rivets (too far back, pressure on the front of the sit bones). You also don't want to be sliding forward or back. Once you get used to that feeling of resting stably on your sitbones, you will hopefully start to learn to tell if a seat is really supporting you properly. You might have to try a few before you find one that's right.
Also, yes raise your seat, you need full leg extension. Rule of thumb is you should be able to just graze your heel on the pedal, that way when you pedal properly with the ball of your foot over the center of the pedal, you'll have a good (small) amount of knee flex at bottom of stroke. (And hold on to those clipless pedals, after a while you may want to put them back on. But platforms are fine; certainly for now, maybe forever)
And yes, raise your handlebars too. Get the seat height right, and then work on raising handlebar height until you're comfortable. (unfortunately, higher bars also changes your torso angle and shifts more weight onto the saddle...). 2009 tells me you probably have a threadless stem. For one thing, you want to get it as high on the steerer tube as possible. If there are any spacers above the stem, unscrew, swap around and get that stem up top. If that's not high enough, then I would recommend looking for an adjustable stem, where you can raise or lower the angle, hopefully enough to feel right.
And take a few pics and post them! That will help us give advice. As they say around here: pics or it didn't happen!