The critical part is that when you ride, you never hyper-extend your knee joint, it should always be a little flexed. The heel-on-pedal measurement is a useful way of preventing hyper-extension. You actually ride with the ball of your foot on the pedal. The angle joint should be whatever is comfortable for you.
Jeans have thick seams and are not ideal for cycling. Cyclists generally require more supportive underwear. I usually ride in cotton briefs and polycotton cargo pants. For longer rides I use padded cycling shorts but I dont think you need these for everyday riding. I find that boxers let things drift around to much.
You also need a saddle that fits your shape and style of riding. Saddles should support your sit bones, not the squishy bits inbetween.