I just replaced the timing chain on my 2011 Mini Cooper S and I also changed the serpentine belt and all 4 spark plugs. I started the car and it ran for a few mins. then pushed the gas a little to rev it and the car died reading my fixed diagnosis tool it shows that I have cylinder 1 and 3 misfire so I pulled the plugs out on those cylinders and they are black so I tried putting the old ones back and now the car won’t start and the plugs on cylinder 1 and 3 still come out black can’t figure out what the problem is.

 

Having just replaced the timing chain, I would suspect the timing is off.

 

Did you torque the crank bolt properly? Maybe it slipped if not.

 

Yeah I torqued and torqued to yield crank bolt and both cam bolts and after having the plug issue I checked and it is still in time

 

Can you confirm that when you check the timing, your flywheel tool is located, the cylinders are all equal height (with straws or similar in the sparkpulg holes), and the details on the cams are both pointing up in the centre. I ask because it is possible to be 180 degrees out and to be on the wrong stroke.

 

Yeah had the pin in the flywheel used coat hangers the same length and even and camshaft locking tool in place the in and ex marks on top

 

Take out your valvecover and check timing again, using flywheel key and cam lockers, I'm betting your exhaust cam gear slipped. On that TTY bolt, though FSM says to torque it and then apply 90-degrees over, mine slipped after a few turns. I went back and bought MINI Genuine bolts and torque it to 180-degrees over just like the intake cam gear. Now there aren't any issues.

Also, check your cam bearing cap torque specs. Make sure they are not too tight, they only need 84 in-lbs. I learned that if they are any tad bit too tight, it's hard for me to hand-crank the entire chain drive to check operation. But once I fixed the torque specs on the cam bearing caps, they got loose and it's much smoother to rotate all cams and crank. This resistance may play part in your timing bolt slippage.

By the way, if your timing does slip and is giving you problems, then I'll suggest you check compression, too. Bent valves may be present. Just precautionary, because mine was like that and I couldn't get it to start. After I fix in the new valves and reset timing, got it all recovered and running perfectly.

 

Edit: Re-read OP, my answer not valid

 

did you check the ground strap on the motor mount? also the green wire at the back of the valve cover?