your config bench tests fine. You do have Anti-lag turned on though for some unknown reason.
Go to Extras -> Advanced ALS and change the "Input channel used" to DISABLED.
If I'm not mistaken your Injector staging "Rate to calculated PW" should be 86 not 35. This is because it's in 0.4% units. The calculation is 34.375%, but you need to divide that by 0.4 to get it into 0.4% units. If I were you I would have the open threshold to be 110 kpa, or maybe even a bit higher than that. You have 75 kpa now.
I tried all of those settings on the bench too and everything looks great. It's great to play with the pressure a bit and see the secondary channels come on.
Note I didn't touch a MSQ file at all. I loaded your configs the proper way and everything works great. Pulse width is about 6.5ms at 3000rpm & 109 kpa. It drops to about 1.8ms once it hits 110 kpa which is what I configured as the secondary activation point. 1600's are big secondaries. :-)