Not wound any Jaguar pickups, but they look like a type of strat pickup.
The flange is the width of the flatwork, measured at the top.
If you are not taping the bobbin magnet core before winding you may be having some shorting between the wire and the magnets.
Your pickup height seems very tall. Tall makes a bright pickup.
A typical strat pickup magnet height, measured between the flatwork, or between the flats, is .430 inches.
I would try to shorten the pickup height some, and tape the magnet core before winding, and try again.
The Estimator fill factor value has to do with how much wire will fit on the bobbin with between 70%-100% scatter.
Scatter is how many turns per layer. The less turns per layer, will fill the bobbin faster, than more turns per layer.
It has to do with the overlapping of the wire, as it builds up on the bobbin.
Magnet type will also effect tone, and brightness.
A2, A3, would be warmer sounding than A5.
Select magnets depending on what tonal qualities you're shooting for?
A5 is the most common rod magnets used.
**Anyone else making Jaguar pickups, please jump in!