Essentially you are asking "what are the laws of Ikar V'tafel?"
Indeed they are quite complex. I'll be following your question while I answer this. Don't treat this as a definitive guide, but this will contain lots of info that'll help your case. (and as always CYLOR)
Determining Ikar vs. Tafel
I heard that the correct thing to do when you have a mixture like this is to go after the majority of the mixture, and say the beracha of that food to cover the entire dish. I also heard that if there's mezonos involved, even a minority, the whole dish automatically becomes mezonos.
You heard correct, but that's incomplete. Here's how it generally works (by generally I mean to exclude certain other types of Ikar V'tafel):
Foods containing Wheat, Spelt, Oats, Rye, or Barley
If a food contains one of the 5 species of grain (not e.g. rice) we generally simply say that the Mezonos is Ikar and all the other foods are tafel.
However, there are cases the grain is not there for nourishment or flavor, but for some external purpose (like a binder). For example, gefilte fish is Shehakol even though it contains grain.
The first step is to determine which of the foods is the ikar (i.e. the food specifically desired). The tafel is the food that is used to enhance the other food. This of course is subjective.
In cases where there is no clear ikar, we then look for the majority. E.g. a fruit cocktail: it would be very hard to say one fruit is the main. So we would look for the majority fruit and make the Bracha on that.
Extent of Ikar V'tafel Exemption
Then, after finishing up my bowl - or even midway through it - what if I get an urge to munch a handful of raisins? Or drink a glass of milk? Assuming I made the beracha of mezonos on the bowl of cereal, which included the raisins and milk therein, must I make a new beracha on the glass of milk or plain raisins?
In the case of cereal with milk, the cereal is generally the ikar and milk tafel. In such cases, the cereal exempts the milk, and even a small amount of milk that's leftover in the bowl. However, if one purposely added a "considerable amount" of milk to the cereal because he/she wants to drink the milk, then another bracha may be required for the milk as well.
According to this, it would appear (I don't have a source) that in your case - all the more so - you should make a separate bracha for the milk. [It would be super-hard to say that the milk in the glass is being drunk to enhance the cereal].
As far as fruits in cereal: raisins, and other small bits of fruit would seem to be tafel (provided they are serving the "enhancing" function). Bananas and larger are a bit more complicated... (CYLOR here)
Bracha Achronah in Ikar V'tafel
And what about the beracha acharona? When I say al hamichya, should I also include al haetz for the raisins?
Once again a fascinating question. Generally speaking both the Bracha Rishona and Achronah are covered by the Ikar (and exempt the Tafel) - provided it's a case of ikar v'tafel. So no.
However, the exception (which would rarely apply here) would be where you eat less than the proper shiur of the ikar. In such case, since you cannot say a bracha achronah for the ikar, you would say it on the tafel (assuming a proper shiur was eaten).
If there was a kezayis of cornflakes, or a revi'is of milk in the bowl, must I also make a borei nefashos?
Sorry, I'm not sure I understand what you're asking. Assuming you're asking "do I need a bracha achronah on the tafel as well?", see what I wrote before. If not, please explain in comments...
Arrrggh! Maybe it would just be easier to make hamotzi and be done with it...
Believe it or not, that would also be a case of Ikar V'tafel (although a simpler one).