Aftermath of Metering/Timing actuators. HELP!

[Grizzly]

Ok heres the scenario.
Took off both metering and timing actuators to check them as I was losing fuel mileage and power and idling rough. I found 3 worn and with side play. 1 Metering and 2 Timing. Bought new put them on. Trucking ran like dog shi#t and threw a fuel rail pressure code and was chugging black smoke. The truck eventually died and wouldn't re-start.
I pulled the new ones I bought and went back and got my old ones back which are now re-installed, as I figured 1 (not knowing which 1) of them was bad.
Pulled the DPF and DOC which were thoroughly caked with soot by now and took them to be cleaned. Which the DPF has now been deemed not cleanable and trashed. So theres $2100 gone.
Since I'm told the truck has to run for AT LEAST 10 minutes to clear stuff up, I'm now running it with the DOC and DPF removed. I got 5 solid minutes out of it (as I am now completely overly paranoid the truck is going to blow up, catch fire, ruin something else I don't have money for) (I also only ran 5 minutes as it is clouding my neighborhood too, as well coating my driveway and house with soot, its a flippin mess) and got 2 egr temp sensor codes, which I expected, and another fuel rail pressure with the red shut engine down light on the dash.
During this time it at least doesnt sound like the a rod is trying to blow through the side of motor but its loping in idle. From 6 to 11 and back. Up and down, Up and down.
So the questions are:
A: Is this still normal, do I keep pressing on letting it idle until the soot clears, regardless of the dash light and codes?
B: Is doing this now clogging up the rest of my EGR system.
C: Is this now clogging up my EGR valve.
D: Is this now clogging up my EGR cooler.
Anyone else do this type of stuff on the fuel system and have to go thru this.
Please give me ALL details of what I will incur or should do.
Many thanks for help!