First, I wanted to say that I am new to NAM and this is my first post. With that being said I have searched as much as I can to find a similar issue, but none describe my issue so I am posting about it. If this is the wrong place or the wrong manner to post issues, then my apologies. Please point me in the right direction.

I have a 2008 Mini Cooper Clubman S R55 with a long list of modifications (listed at the end) that is haveing a rough idle. When starting the mini, and it dosent mater if it is cold or warmed up and I turn it off and re start, it has a rough idle. The rough idle seams to last about 1 min and 20 seconds give or take. At that time it throws check engine light with several codes mostly misfire(usually P0300, P0302, P0301, P0303, B2aaa) and smooths out the idle after throwing the codes.

Now the catch is, if I do not let it idle long and just drive off, I do not end up throwing any codes and as long as I drive just a little bit (haven’t determined the magic distance) I can stop at idle and it is smooth as normal.

I have a brand new engine build as right around 100k miles blew the ring land on Cyl 1 and was forced to rebuild or scrap the car. With this re-build most all engine parts were replaced. Most of the ones that I can think that you guys may suggest that were replaced are as follows: HPFP, new coils, new plugs (1422 colder range plugs), new valve cover, new VANOS sensor, new camshaft position sensor. Lots of other new parts, those are just the ones that I can think of that are relevant. With all the new parts, I know they can still come from the factory with defects, so I checked the fuel pressure and motor off(in tank pump) it sits at 90psi, and running at idle (HPFP) it sits at 712psi. Which both appear normal. I double checked the plugs gap and they are sitting at .22 gap. Checked the AFR’s and under heavy acceleration the lowest it drops is 11.5/11.6 area which appears normal. I have pulled the valve cover and double checked the timing and everything is good. I have checked the compression and all is good. Can’t imagine there could be carbon build up as engine only has 4K miles on it.

I am at a loss as to what is causing this issue. Any suggestions or recommendations are welcome. I did all the motor work my self (except machine work) and know my way around a car well.

List of modifications:
Carrillo forged rods
CP forged 9.5CR pistons and rings
47mm JMTC polished Turbo puts out 22.5 psi boost
Ported and polished head with 3 angle valve job
Catless DP
3” DP back exhaust
Larger FMIC
AEM CAI
Hot side muffler delete
Noise maker delete
Manic stage 2 tune with SPS switcher (I need stage 3 as stage 3 is a custom tune but don’t know if maybe this may be part of the problem)

Yes, I have had the issue since rebuilding. I did re-check the timing and all was correct. The compression is less compression at 9.5CR vs 10.5CR of stock so if anything it would be running lean which it is not. The spark I can only assume is strong enough as with the manic tune, i am using the recommend spark plug for the tune.

The HPFP is new installed by Mini under warranty. The cylinders are not flooded. I did not replace the fuel injectors in the build but this motor is direct injection and adjust fuel according to the needs of the engine based on DME readings and is not like a fixed injector where it only flows a certain CC (example 350cc injector). I don’t know/ have a way to read individual injector readings of flow on this motor. Also, like I said in the original post, it smooths out after a certain amount of ideling and throwing the codes or just driving.

The tuning makes sense to the rough idle, but it does not make sense to me about it throwing the misfire codes if it is left to idle.