Diesel Bombers - 6.5 diesel hard starting/limp mode

I just replaced my valve cover gasket on my drivers side, so I had to take the injector lines off. I also changed the fuel filter while I was in there. now I got the truck started, and I let it idle for about five minutes. Then I drove it to the store about 15 minutes away and let it idle for another 5 while I grabbed some antifreeze. and drove it home. it still starts hard, but it is a consistient 8 seconds of cranking then It fires right up. I notice a small amount of black smoke while in gear at a stop light, then when I accelerate it blows a lot of black smoke I am making plenty of boost I just don't know where to go from here.

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this is a 98 chevy 6.5 diesel too

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1. Describe the problem you are having in detail:
I changed the valve cover gasket and fuel filter, and now,The truck takes longer than normal to start and the truck blows a lot of black smoke.
2. Year of truck/engine.1998
3. Odometer reading (indicate miles or kilometers). 224xxx
4. Indicate the model number on the Injection pump (starts DS4 or DB2......).DS4
5. Indicate if you know if it’s a 1500, 2500, 2500HD, 3500, 3500HD. K3500
6. Do you have an EGR on the engine? (An F or an S engine code 8th VIN digit)no
7. Air Filter condition (visual check).Clean
8. Fuel filter condition (freshly changed, mileage since changed).New

9. Location of PMD/FSD? (ex. on pump/remote over intake, behind bumper).on intake
9a. If remote mounted, describe wiring harness (homemade or purchased from which vendor).
9b. Indicate the location and condition of the FSD/IP grounding wire. intake plenum
10. Outside Temperature (C or F). _____ 75

11. Service Engine Light while running?- on
11a. Service Engine light does glow during start/cranking/bulb check: yes
12.Have you scanned for engine codes? yes
12a. List exact results on engine codes. Crankshaft sensor
13. Condition of Battery terminals (removed, cleaned and tightened).cleaned
14. Known condition and age of Batteries.good, 2010
14a. Are batteries a matched set of same age?yes
15. Condition of Major Grounds (removed, cleaned and tightened)Clean

16. Does engine crank, or "turn over"?yes
16a. Does engine start and run?yes
17. If engine does not start- Crack injector line: do you have fuel? Yes/No
18. Does your Wait To Start light come on?yes
18a.Number of seconds WTS light is lit.3-4
19. Engine Cranking speed (if you have an accurate tachometer).

20. Are you experiencing Stalling?nope
20a. Describe the event (upon startup only, down the road, hit a bump, etc...) on start up and when I accelerate
20b. Do you notice loss of dash or instruments?no
21. Check turbo inlet and air filter for obstructions.
22. In a no-hot start, pour a bottle of room-temp water on the injection pump. Does it start now?
23. Lift pump test - Describe results. good

24. Upon cold start, does the radiator hose get hard quickly? No
25. Upon cold start, do you have excessive white smoke? No
26. Do you have excessive cranking time before the engine starts? Yes
27. Have you used the block heater? Does it affect engine starting? (only try for starting problems). Don't know yet
28. Are all glow plugs in proper working order? yes
29. During hard acceleration, do you have excessive black smoke? Yes!
30. Do you have any unusual exhaust smoke issues?its black
31. Turbo check out - turbo builds 12# of boost real quick
32. Indicate fuel that you are using: Bio-Diesel, #2 Diesel, SVO/WVO, otherdiesel #2 diesel
32a. If running Veggie Oil fuel setup, indicate details of your conversion (homemade or packaged system).
33. Are you using any fuel additives? If so, please list.
34. Upon unscrewing fuel cap, do you have a large vacuum formed in the tank? Yes/Nokinda
35. Do you have any service history available that might pertain to the problem you are having?
36. Please indicate any modifications to the vehicle that might help us diagnose better. turbo master

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check engine light is p0335