Last year, I was on this forum and received a ton of help after my injection pump gave me a headache. The motor ran quite well for its age before problem, tired but strong enough for what I need. During the pain of having a rebuild and then a check that the pump (or I) hadn't gone goofy, I discovered the problem to be that bloody 76 cent sheer pin dammit. But whilst trying to start with the timing way off, I used quite a bit of ether and when the motor eventually fired up, it wasn't very pretty at all. Rough, tons of black smoke at first that reduces once it's warmed up. Sounds like 1 and 1/2 cylinders !!. Today I put a boroscope down the injector ports, quality is poor but #3 cylinder looks nuts, I think I've destroyed the piston !! Attached are some pix of that cylinder. I have the original injectors being serviced in place of the cheapo chinese ones I got on Ebay. Budget considerations after the pump was $1200 !! So, opinions and suggestions of the compassionate kind will be appreciated. The ol' dear still has a small ammount of work to do before I can scrap it.
Do a compression test. It will tell you a lot. It sounds like the injection pump timing is OFF.