2005 X3 3.0i morning startup problem

Hello,

I have been trying to do a little research before bringing my X3 to the dealership for a service. Here is the problem I have been facing-
(1) Every morning my car starts fine and stalls after about 30 seconds
(2) Then I start it again and it stalls. This repeats 3-4 times, more on colder days.
(3) All this while the temperature needle slowly rises, and once it reaches about half way, the car runs fine for rest of the day. Even if I just drive it for 10-15mins and park it for 8-9 hours.
(4) For rest of the day, the car works just fine with the temperature jumping to about half way as soon as I turn the key.
(5) After parking it overnight, the trouble cycle starts all over.

I drove the car to an indie mechanic who recommended a DME replacement from the dealership, here are the codes-
2869, 28B2, 27A1 and 2796, related to service bulletin 12-49-06
Other codes are 2830 and 3C1F

Also, the battery is replaced about a month back.

Any advice is much appreciated.

I am super comfortable with computers, can I re-program/flash my DME (and other modules) at home?