ah yeah its not that it 'hits' later, its the whole diameter of the pipe needs more energy coming out of the port during blowdown to reach the same amount of pressure in the compression of the wave.
you can think of the compression wave pressure like amplitude or height of a wave on the beach. in very broad terms the length determines the timing of the pulse bouncing back and returning to the port, the diameter of the pipe determines how much energy it is capable of returning and bouncing back. a bigger header takes a bigger 'gulp' of air and can reach higher supercharge pressure, which is why french pipes have massive headers, but they need a lot of the energy from the exhaust/power stroke to be blown down and fed into them in order to create the energy in the wave they need to power them.
a bigger pipe diameter needs more blowdown energy to reach the pressure that it needs to function at peak efficiency. A smaller exhaust header keeps the pressure high in the pipe so the compression wave has energy when it comes back to the port to provide the supercharging effect, but at high energy it limits the volume that the pipe can suck out and return to the cylinder.
I dunno if i'm explaining this very well, i'm really tired and pretty drunk and its like next level thermodynamics type shit here so i'm probably not making much sense, but my general rule of thumb is:
small (diameter) header- small blowdown, big header- big blowdown
longer pipe- low rpm, shorter pipe- high rpm
sharp expansion of cones- hard hitting/narrow powerband, gradual expansion of cones - wide powerband/ less 'hit'
the modded estoril should be a perfect pipe for your setup, like i said i designed the head but Blake/Dos did all the testing and i'm not sure who out there in ATL ran it or what their setup was but i've gotta say 40 sounds miserable since i know some stock M1's that run solid mid 40's. i don't think the pipe is your problem. I also know that chad burke has run some different kits on M1's and might be someone to talk to. unfortunately he doesn't post much on here anymore but you can probably message him.