my 9400 cat wont go past 1000 rpm

irecently had to replace water pump in this beast and 2 days later the rpms wouldn't go past 1000. I let truck idle andf warm up - problem went away. now went to use it today and again the rpm wont go past 1000. I did find a broken battery connecter and replaced both filters. im thinking its an electrical thing - note if use cruise control its same reaction - not past 1000

 

I did both filters and did find 1 broken terminal in battery box for ecm ground

 

I did find a bunch of black garbage inside the secondary filter - I find that unusual due to the primary davco one seemed rather clean. wondering if I have that crap growing in the fuel system