changed cp3 now have engine tick or knock.

like the title says change my CP 3 now my truck ticks or knocks passenger side middle of the engine don't know why. I changed back the old CP 3 the original still ticks. sent the one cp3 out that I had bought had it tested came back nothing wrong with it ended up sending them my original one as the core so now I have a new one that still makes my engine tick.
the truck is a 2005 ram 2500
I've heard of people read indexing the cp3 I have not tried that but before I get that far I need to change my crank shaft gear when I dropped my lock washer in to the gear case it went through the gears and broke two teeth off.

Looking for suggestions on why it is ticking...

sure would be nice to have my truck back together it has been a part since around Christmas

...

ASh%t talk about bad luck! There is no indexing the CP3 you more than likely have a bad injector and the new pump is giving it more fuel than the old one did. Send out your injectors when you take the gear off which will be a hell of a hard job Die grinder cut a slot in it hit it with a hammer! POP!! Heat the new one and pray you get it on right the first time "All the way" Besides the crank what other gear got eaten? CAm
Oil Pump??.......

I put brand new bosch 50hp injectors and cross over tubes in my truck also at the same time I changed the CP 3.
and i have a brand new common rail with the pressure sensor and pressure relief valve in it.
all the other gears look fine.
i also checked and it did not jump time