I know you're exploring other possible culprits for the discomfort now, but if you come back to handlebar position, it might be worth getting a higher rise bar if you find riser stems to look goofy. 50mm riser bars are easy enough to come by, but there are brands out there, like stooge who do their klunker bar in 75mm and 100mm rise versions (somewhat pricey, admittedly). For the more budget conscious, you could get a Motocross handlebar (22.2mm clamp) fairly cheap, and use a BMX stem (22.2mm clamp diameter) to fit it on to your bike.