Since you don't know what the fit issue is, but there obviously is one, go to a real bike fitter. Ask for recommendations.
Since the knee is inflamed now, and simply fitting the bike correctly isn't going to cure that immediately, stop riding until you get the fit. Don't make it worse. Act now. Also buy some sort of bike computer which will show you cadence. After the bike fit, every day if possible go for a 30' easy bike ride, pedaling ~90 cadence. You should not be breathing hard, just rather deeply. Do that until the knee stops hurting. It's odd, but it is usually just one knee that starts acting up after a bad bike fit.
In the future, try to ride 80-90 cadence until you run out of gears climbing.
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