I'm confused as to why /Q works but Q doesn't? I'm sorry for being a noob with this stuff, I was hoping you could try to explain? My understanding is that the pulse sent to the flip flop becomes inverted by attaching /Q to the data input pin. So the pulse leading edge hits the IC, it says turn on but because /Q is inverted and is attached to the data pin it stays off until the low end of the pulse hits which is not until the end of a 2 second delay due to the rc timer circuit and hence I get my long press to turn on the power. If I use /Q to drive the gate instead of Q wouldn't that completely ignore the delayed start I'm looking for?
Looking at this more closely I think I'm seeing another issue. The flip flop doesn't remember states, I want to make sure that the board isn't powered on when plugged into power to charge the battery. I've got an RC circuit on the CLR pin (R6 & C6) I'm just insure of whether this circuit is pulling the pin low or high. I believe its pulling it low but I want to be sure.
You have the flipflop configured to come up with Q low. You've done that with the R/C on /CLR. But /Q is *always* just the inverted state of Q. So the flipflop will come up with Q low, but also with /Q high. High is the state needed on the mosfet gate to keep it turned off. When the first long button press occurs, CLK will go high, and the state of /Q (high) will be latched via the D pin to Q, which will bring Q high and /Q low, which will turn the mosfet on. Both Q and /Q change state *immediately after* the rising edge of the CLK. Nothing happens on the falling edge. You get a falling edge when the button is released. Then the next long press produces another rising edge, which brings /Q high again, which turns off the mosfet.
Your NPN circuit is just an inverter for Q. When Q goes high, the NPN brings the mosfet gate low, and vice versa. But you already have something that always produces an inverted version of Q, and that's /Q. It should work exactly the same, but without the extra parts.
I think you would find it really helpful if you could breadboard stuff like this and test it out with through-hole versions of these chips.
Edit: You could also drive the mosfet gate directly from Q, but you would need to move the R/C over to the /PREset pin so the flipflop would come up with Q high.