There is quite a lot already in this thread however I have picked a few points from the OP to comment on:
To get good diesel combustion a rapid start and end of injection is required as well as good atomization. Using an inlet port in the side of the pump cylinder allows the plunger to get up some speed before injection starts. A separate ball inlet valve like Minh uses should close almost as soon as the pump piston starts rising. As his pumps are cam driven this works. I am not sure how rapidly your solenoid system will accelerate.
The volume of fuel to be injected is small and the pressures are high so any flexible item or trapped air will cause poor or no injection. With a plunger type pump may be difficult to get the air out of the clearance between the plunger and the barrel. An elastomer O ring may also deflect sufficiently to cause problems. PTFE of HDPE may be better.
You are looking at a ~50cc cylinder which is more than double the size of mine. I am using a 2mm pump plunger with a working stroke under 1mm (difficult to measure with a helix controlled pump so you could increase the bore to 3mm. A 1mm plunger will have quite a long stoke and may suffer from Euler buckling, a risk at an L/d of more than 5.
I would suggest that you start with a simple hand operated injection pump to develop the injector design before you move onto your rather interesting solenoid design.
There is a lot of information, which I am sure you are aware of, in this thread:
https://www.homemodelenginemachinist.com/threads/request-injector-designs.36273/
I am not doing and further fuel injection development at the moment as I am building a 20cc Junkers style opposed piston two stroke diesel.
When it is ready to run I will need to do some more work on improving the atomization.