NPN transistor slow to turn off even when operated outside of saturation region

The main problem is likely to be Miller capacitance (internally 10 pf or so between collector and base) and the 15 kohm base drive resistor. CR time is going to be 150 ns due to that alone and will remain delivering current into the base for several CR times while the transistor is trying to turn off.

Try putting a reverse diode across the 15 kohm resistor such that when the input goes low it removes charge via the diode rather than through the sluggish 15 kohm.

I'd also consider using a potential divider at the base to deliver a lower impedance signal to the base. If you clock is 3.9 volts, potential divide down this to about 1 volt with a 4k7 across base and emitter to see what improvement that makes.