Salam Yaser Sb.,
Nice to see you are back on the project. you are right, you need to go to your machinist. Take the entire assembly to him so he can see what is going on. Without seeing the engine, I am thinking that when you turn the engine, the chain is turning the cam also. I would suggest to remove the chain and turn the cam by hand separate to the crank and then turn crank separate from the cam. You will find out which is the one with the problem. My obvious guess is that the line of one of the two is not straight or you have ovality on the bearings.
You machinist will be able to figure it out. I may be wrong but my mind goes to the cam bushes that were not line bored. I noticed that your machinist did not have a dial gauge. To get a proper idea of what is going on you may need to check your engine with a setup similar to this.

If your mashinist uses a wire and feeler gauge to check the trueness and then I would strongly suggest to find another machinist.
If your problem is the crank shaft, just off the cuff, usually crank issues are one of the following:
1 - Crank is not straight
2 - Crank main pins are oval
3 - Crank case line is not straight.
4 - Main bearing clearances not correct
We used to take measurement of crank web deflections to figure out what was going on. But in your case the crank is too small to fit a dial gauge in the web of the crank.