Deutz-Allis 6265 not running smooth

Hi everyone, I have a deutz-allis 6265 that has around 3k hours on it. We serviced it last week and after changing the fuel filter we could not get it primed good. Finally got it to start but it was missing bad. After trying several different tricks we finally found that the steel braided hose from the fuel pump to the injection pump was partially collapsed. After replacing the hose, it runs much better but it will still miss occasionally in a hard pull but then it clears up, and sometimes when you throttle it open a small puff of white smoke comes from the exhaust. It never done any of this before changing the fuel filter. Supply and return fuel hoses have been replaced. I did remove 2 of the injectors during troubleshooting the first go round but I re installed them the way they came out. Any ideas as to what this may be? Any help is greatly appreciated!
 
Does this have a lift pump? If so, check the pressure and volume.

If practical, temporary a section of clear vinyl hose between the lift pump and the injector pump. See if
there are air bubbles going to the injector pump. Could be a leak in the lift pump or the line between the
tank and the pump.
 

Yes the lift pump is brand new, just installed a few days ago because we suspected that to be the problem at first since it would not prime. But I had not thought of using a clear hose to test for air bubbles but I'll definitely try it! Thanks for the advice!
 

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