The intakes valves clearance is a minor issue that should be done soon (before a lot of mileage is added). But, given you are only 0.001 (1 thoushand of an inch) below specs, this is not enough to cause bad engine behavior. In their design / specifications, BMW has already planned a margin of safety when 0.006 is specified as a minimum setting - however you want to avoid running the engine at 0.004 intake valve clearance - thus 0.005 is the wake-up call to act soon before it goes tighter (they alway go tighter with wear / mileage on these "brik-engine").Ok
I've checked timing several times to ensure piston 1 was at TDC. And as the pictures indicate its in time and has not changed at all since the valve adjustment/bucket swap.
Cam chain sprockets are both vertical pointing straight up. And the slots in the end of each cam shaft are horizonal as outlined in Clymer manual pages 90/91.
My only concern is that I checked the clearance on the Intake/exhaust valves again and 3 Intake valves are tight.
Cyl 1 - 006/006 - Good
Cyl 2 - 006/005 - One Tight
Cyl 3 - 005/006 - One Tight
Cyl 4 - 005/006 - One Tight
Hence, to find cause of your problems, you will have to keep looking or double checks all your previous work. As suggested earlier by H96669, the Motronic relay exchange is a good probability and fairly cheap item to try.
Do you have a GS911 to read fault codes and check all parameters in "real-time" (engine running on center-stand) ?