Hi,
Timing should be straight forward enough.
I see you chalk marked the timing gears to be able to relocate them.
I think I would have started from scratch, removed the idler gear , lined up the TDC 1/4 mark on the flywheel or just turn the key in the crank shaft gear to the top. Then refitted the idler, at the same time turning the cam and pump gears to match the original timing marks. That should then be TDC on one and four with the two valves on four rocking from one to the other and No. 1 firing.
If you are refitting all the original components the Master spline in the quill shaft which drives the pump should locate correctly and it should be sufficient to simply line up the mark on the pump flange with the mark on the timing case.
You could have established which cylinder was injecting quite easily without pressurising the line because the master, (large), spline on the quill shaft always lines up with the injector pipe which is delivering fuel.
It should only be necessary to retime the pump internally if fitting a new one or one from another engine as each pump and engine are a matched pair. New pumps don't have the timing mark on the pump flange and it may be necessary to make a new mark when swapping from another engine.
The static pump timing is set at point of injection which is usually somewhere about 22 to 24 deg. before TDC if there is not a flywheel mark INJ 1/4 or other locator to establish this point it becomes a little more difficult.
Perkins recommend turning the engine to TDC 1 removing the collets from the inlet valve and allowing it drop onto the piston crown.
and to set up a dial gauge on the top of the valve stem, then to rock the engine to zero the gauge at TDC.
There is a table of distances below TDC which relates to deg. before TDC.
Typically on your engine at 22 to 24 deg.
before TDC, point of injection would be 4 to 6 mm below TDC
The required setting is determined by the number on the injector pump ID plate where it says Type.
When point of injection is established, (Hopefully there will be a mark), we come to the internal pump timing.
I have no experience with Bepco after market pumps, and can't understand how there can be no timing circlip.
Normal procedure is to loosen the three bolts holding the pump body to the timing case, remove the small plate from the side of the pump to view the rotor , turn the body till, ( in this case), the letter C lines up with the square end of the circip. Some pumps have a line on the circlip to line up with instead of the square end. Then make your new timing,(chisel), mark on the pump flange.
If there is no circlip I don't know how you get round it except with the proper service tool and injector test pump to create a hydraulic lock and establish the timing mark on the pump flange.
You probably know most of this already but I hope you can pick something out of it which helps.
Good luck.
Fred