@Xulfiqar Thank you so much for taking time to reply in detail 
Actually I handed over the engine to a repairman who claims to be the specialist in fixing engines in Rawalpindi. I didn't supervise him all the times, just took some video shots for my YouTube channel, yet to produce a video, will share once I compile everything.
And I don't know much about such technical things, but let me try explaining what you want to know:
1 did you find a new crank bolt?
If you mean replacing the crank, then NO, we didn't change the crank as he told me that it was fine.
2 did you use a torque wrench on that bolt?
* Couldn't understand
3 what tool was used to tighten the head
I wasn't there so I couldn't see and record them using the tools
4 is the pump from a turbo engine? (Has the boost compensation device)
I am not sure, showed this to Waris Shah lab in Gawalmandi and he didn't say anything so I assume that it is genuine turbo pump. Here's the picture:
5 how did you time the pump to the engine?
Waseem Diesel lab technician on Tipu road made some adjustments and he told me that pump needs to be repaired but first I needed to fix the turbo or get rid of it. However, starting and overall performance got a lot better after he did something to the pump, the only problem left is bad fuel economy, it isn't giving more than 14 km/l in city traffic. Not too much traffic jam and very low rpm driving.
6 does the pump advance timing at 2000 engine rpm?
He increased the RPM to get rid of rough idling but it remained there and instead worsen the fuel economy (AC has been removed since I got the car). So we reduce the idling speed again by making some adjustments. RPM also fluctuate but overall is okay, no misfiring or giving jerks etc.
7 are the injectors set to pop at the right pressu
re? They pop at 1700 psi i recall.
Injector nozzles are worn out, will replace them once turbo mess is cleared.
White smoke appears during cold start but vanishes as the engine warms up.
And yes, there is NO DIRECT FAN which you normally don't recommend
, automatic switch has been installed.
Thanks once again for your time to offer your professional advice!