The bubbles might be coming from the input shaft seal, one way yo easily confirm it or not is to put a electric inline pump before the filter. You could also be pulling air from any of the supply fittings.
The leak from the injection pump could be from the dynamic advance piston cover. I have never seen an VE pump leak where the head meets the body. I have fixed three from leaking dynamic piston covers. You will need to remove the pump to re-seal that though.
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