In pakistan you should be careful.in these two areas. Afghan Border to Peshawar city area... and then Karachi to Iran....
Not only careful. I will advise to skip these two portions. all the other areas of you route are safe.
Don't have information about Afghanistan. But In my view no pakistani guy will think to visit afghanistan.. peshawar to afghan border and balochistan area... on bike...
Safety is the best practice. Life is first.
Also I think instead of just riding. you must focus on visits the areas/tourist locations..
Have a nice and safe journey.
you can go Quetta and Iran Border through train from Karachi and Sukker with loading your bike also on the train.. That would be safe. you can see the scenery enroute. while being safe.
Loading bike on train will only cost 10-20 US Dollars.