Originally Posted by cale

You're the wizard where it comes to fit but I can tell you that flipping the stem put the bars further and lower relative to the seat tube. I'm surprised you mention having raised the seat because a lot of riders might have lowered it slightly. (Lowering the seat effectively "shortens" the top tube.) Any way, your new position, as described, sounds substantially more aggressive which is appropriate for someone trying to find the right fit. The achielles pain doesn't sound good. Drop the seat 1/2 the distance you raised it and see if it helps.