Thanks to everyone that helped me out on this thread, so it turns out the valves were not the issue as they are mechanical. It was the injectors and the Fuel Tank Vent Valve. All replaced and the car runs amazing.

Thank you everyone, great help.

Here are some videos on youtube.

No I havent done that yet as the cover is in the range of $500-600 to purchase. One mechanic said they did a smoke test and found that the cover was leaking but I replaced the cover gasket after that as it was old and hard. How could I do a smoke test at home?

A borescope inspection inside the intake ports on the cylinder head will tell you if a walnut blast is warranted.

Have you replaced the valve cover? It could be a vacuum issue inside the valve cover in the PCV system - just another guess....

My Mini is direct injection.

Walnut blasting of the backside of the intake valves is for engines that have direct injection. The valves of a dry intake charge (direct injection engines)  get more deposits  than fuel injected engines whose wet intake charge cleans those surfaces

The motor fluctuates in idle when in park so I assume when in drive its doing the same thing which would engage the converter and cause the car to hop. Don't believe there is a issue with brake booster. I changed the coils, plugs, HP fuel pump, valve cover gasket. Next I was going to try the fuel filter before I do the walnut blasting which I do not beileve that is the issue as the valves are mechanical and would not cause all this idling issues.

if it happens only when you put your foot on the brake, then this is an important clue .

When you put your foot on the brake, then you are activating the power brake booster . An intermittent vacuum leak in the hoses (or booster itself) could allow extra air to flow into the intake manifold and the engine could speed up. Look at the hose connection between the engine vacuum take-off location and follow the hose to the brake booster. See if there is a crack, hole, or split. Sometimes it is hard to see. Sometimes you cannot see it, but just wiggling the hose (with engine running) at various locations will make the vacuum leak appear. If so, the rpms should change.

Even harder to see is if there is a vacuum leak in the booster itself. I do not know what the dealer would do to test this., but if you cut the hose, insert a "T" and attached a vacuum gauge, you could see if the vacuum reading holds steady or not. The reading will change, depending on whether your foot is on the brake pedal or not, but the important reading is that it should be a steady reading once foot position is no longer moving ( either brake on or brake off) . Of course, if you do this test, the cut hose would need to be replaced no matter what you discovered on the readings. I personally have never done this test.

It wants to go sporadically when I have my foot on the brake, so I have to put it in neutral. Jumping as if I pressed the gas and released and pressed again while having my foot on the brake. Ive taken it to the dealer and spent thousands on assumptions what it could be so I would reach out to fellow Mini goers for some advise. I don't here a vacuum leak that would be noticeable, how could I do a homemade smoke test for the valve cover? Before it sat for 3 weeks without driving it it ran great, since I let it sit for 3 weeks in the garage this started happening all of a sudden.

It wants to go sporadically when I have my foot on the brake, so I have to put it in neutral.

What fo you mean jumps when foot on the brake? Do you mean rpms  jump around ? Running jumps between smooth and rough? Do you have a vacuum leak in the power brake booster hoses or unit itself? 

Any suggestions?

Yes. That’s correct, the issues only occur when at idle or stopped at the light. If I am driving on Hwy or street the vehicle drives as it should. It also has a tendency to want to jump periodically when I have my foot on the brake.

Ok, it sounds like you are seeing the P0300 error code (please confirm).

Many different causes can trigger this code, but the more common ones are:

high pressure fuel pump
vacuum leak
carbon buildup 
fuel injector issue
coil issues

Yes the engine light is on, codes say misfires in all cylinders. Has 180,000km but very well maintained.

Yes there are codes for misfires and engine light is on. 180,000km

Does the check engine light come on and are there any error codes recorded in the computer?

How many miles on the car?

Hi everyone, I have a issue with my 2010 mini S, it sat for 3 weeks and once I started it thats when the rough idle up and down started, in park she would barely run but once warmed up and drove it the car was fine at 60km and on the hwy, once I stop at a light it all starts again and I would have to put it in neutral for it to stop from jumping forward as it was idling rough. I did the sea foam cleaning and turbo clean it did get better but still rough. I did notice there was too much oil in the motor and found oil build up in the pipe to the throttle body and small amount in the turbo. Does anyone know what I can try next? I have replaced the Valve cover gasket, plugs, coils. Looked at the back of the valves they are not that bad as this issue would persist even at high speeds but does not. I drained the oil which was about a litre over. Could some sensors been affected with oil being pulled up into everything? The HPFP was checked as well and its fine. 4 shops cant find the issue and just say the codes read misfire in all cylinders.