A couple of ideas here. Firstly does an HR3 have a decompression lever/mechanism? If it does check the adjustment. If the valves are being held even slightly open it will not achieve adequate compression for combustion in those cylinders.
Second: check that the exhaust valves are not sticking, carbon build up can cause valves to stick slightly open, no compression no combustion. If you can crank it over by hand you should be able to hear air hissing out if there is a valve leakage issue.
Third: when you installed the serviced/replacement fuel injector pumps did you do a spill test? Not all pumps are identical, it is important to get the timing of these correct, I believe they are adjusted by adding or removing shims between the bottom of the pump and the crankcase block.
Let us know how you go,
Bob