Give it some time and let your LBS adjust the bike to help ease the transition while you're getting back into shape.

I began riding again in late August after a 30+ year hiatus. Never thought I'd ride again at all, let alone enjoy it, after a car wreck busted up my back and neck, including a permanently damaged C2 vertebrae. I got a comfort/hybrid style bike with upright bars, which suits me for now.

Took a month of riding 1-5 miles three or four times a week just to begin to feel like I was making some progress. Just as I thought I'd plateaued and wasn't going to improve in conditioning, I began some steady improvements after about five weeks. I knew it was gonna hurt, but I was careful to avoid too much stress on the joints. I used granny gears a lot on hills, and got off to walk up when my chest was about to explode. So I've managed to make it to three months without much serious pain in the joints, back or neck - just the usual sore muscles now and then, and a couple of days with spasms in the back and neck.

Now I'm at the point where I get antsy if I don't have a chance to ride at least 20-30 minutes a day, even if it's only a circuit around the block or a couple of errands. And if my conditioning improves I might reconsider lower bars next year. But for now I'm better off sticking with upright bars - although occasionally I'll lean forward and rest my forearms across the bars to reduce my profile into the wind or on long and/or steep climbs.