LAshotgun

I feel pretty comfortable on my bike. My stomach and back are fine. I notice that my glutes and hamstring tend to get sore but my quads never do. Should I lower my seat some?

Road Fan

Read through the forum about seat height - we've got about 5 methods documented here. Try using the one about heel-on-pedal with leg straight to get a reasonable starting point baseline of saddle height.

What kind of bike?

Carbonfiberboy 

Probably not, but do as above. Also push forward at the top and maybe push more on the way down. Most folks get sore quads just fine, so you're a bit of an oddity that way. Try standing more. It's good to be able to turn about a 70 cadence for a long time out of the saddle. Strengthens the legs and improves balance and conditioning. I make it a point to stand about 1 minute in 10 if there aren't little rollers that would make me get up anyway.

equinoxranch

Question to LA............... Chiefly, what is the height difference between your handlebar (top) to that of your saddle which I hope is NOT tilted down, btw? Your saddle height (and horizontal) might be well within reason (in other words just fine) at an appropriate length/relation to the pedal............. Whereas you might be realizing undo strain to the glutes and hamstring as you could have too low positioned handelbars (relative to saddle height) which demand you bend over too much thus straining those muscles be same when on the tops, hoods or all the way down. Additionally, not knowing your size/physique but are you too forward in your seating position(s), especially if you have a long femur............? Where is your saddle positioned on the seat post........., central, forward, all the way to the rear? If you are ultimately way forward on just that alone - knee in front of pedal spindle - this might also be the culprit.