1. I have been moving things around on my bike trying to get comfortable and am having pain on the lateral/outside portion of my popliteal fossa (back of the knee), and my quadriceps near my knees are fatiguing very quickly during rides

2. when doing the heel to pedal method for seat height do you want you heel just barely touching or should you have a solid footing and grip with the heel

3. on the 109% of inseam for seat height adjustment do you measure from the top of the seat to the center of the crank, or top of the seat to pedal when its down and in-line with the seat post?

For your popliteal fossa, you have to play with your cleat positioning if your saddle height is correct.

The 109% fit approach would be from the axle of the pedal at it's lowest/furthest stroke (not 90° from bottom). I fit bikes professionally, and I find the goniometer to work best (knee angle 27-37°) because it takes the factor of femur & tibia bone lengths. Now, to get this accurately you need to observe your pedaling style (heel height). You also need to be measuring the shorter of your legs.

P.S. The heel to pedal method is only for a bike shop setting someone up for a test ride.