Converting 6c (3s2p,4.5v) DC motor to 1s4p 18650 charging/protection
A 25-W motor running at 4.5V is drawing 5.5 A. The effective motor impedance is therefore 4.5/5.5= 0.82 Ohms. This is a serious load for small consumer-grade batteries.

For example, specifications for Energizer D-cell (E95) say they have 200 to 400 mOhms ESR. Even in best case of 200 || 200 mOhms = 100 mOhm for a parallel pair, times 3 for 3 cells, gives 300 mOhms of battery ESR best case. 

Therefore, the 820 mOhm motor will take about  4.5 V / (0.82 + 0.3) =  4 A of current, and the running voltage will be about 4*0.82 = 3.3 V. And 1.2 V will be dissipated on internal ESRs inside the batteries.

The Li-ion 18650 likely has under 100 mOhms ESR, and the drop will be only ~0.5 V, so with a freshly charged cell the motor must be running at 3.7 V, and thus the it takes more current and likely runs faster. So the Li-ion is much better choice for this application.

Now, since the motor is rated for 4.5 V, you shouldn't use any "trimmers", this is a very bad idea, waste. You can run your pump directly from 18650 cells.

Regarding "protection" and stuff, just buy cells with built-in protection, it is usually listed even by junk merchants. 

One little problem is total capacity. With the 25-W motor your 4P battery will run likely no more than for 1.5- 2 hours (4 cells with typical 10 Wh capacity give you only a 40 Whr battery). If your current design (from 6 D cells) runs the motor at 3 V and this is sufficient for overall functionality, you might want to consider to reduce the driving voltage from Li-ion cells to that value using a buck switching regulator.  

But if you want a really nice enclosed device with charging capability, you would need to design in both charger and BMS. And for 8 hrs run time you will need a battery with ~20 18650 cells, as Tony rightfully noted. Maybe you should be considering bigger Li-Ion cells, automotive or bike style, or sealed lead-acid batteries.

Alternatively, you might save youself a lot of time and money by looking for a professional design as Goal Zero Yeti portable generators or similar, Suaoki, Webetop, Paxcess, etc.