Hi Jacqueline, welcome to BW forum
First off, PUPD is a method of last resort, only to be used when you've tried shush/pat consistently for at least 2 weeks with no improvement. It should almost never be used when LO has reflux. It should also not be used if you don't have a solid routine for LO. Its also probably not the best if you're worried about slow weight gain as PUPD can take a lot of energy for LO.
40 min naps can be developmental at this age, but they can also be related to too short an A time - LO is undertired which would be my bet since he's 4 months old with 1.5hr A time (a very common scenario with the "4 month regression").
So, can you please post your EASY - what you're aiming for and how your last few days have actually gone with E and S times so we can see how its going and pick out any patterns. I see your concern re: 3hr feeds and suspect you're working on 3hr EASY with 1.5hr A times which is not suitable for a 4 month old baby.
Just a few other questions:
How is your baby fed? Breastmilk/formula / from breast/bottle
Is the reflux controlled? If so, how?