Wow after a whole week there is STILL not a complete answer.
On the I've gave a detailed explanation about genotypes and phenotypes about a month ago on this
very subject.
As for the Eisuke's blood type changing,
here is an article on bone marrow transplants.
Basically, in an ideal case a donor with a matching blood type would be used, however in cases where a immune reaction would occur, the immune system of the recipient would be suppressed and all traces of the recipient's anti-A and/or anti-B lymphocytes would be destroyed by high doses of chemotherapy.
Essentially, the immunosuppression only allows the recipient to accomodate for new antigens, so the recipient's blood type does not always change after transplant. For example, a recipient with O type blood receiving AB bone marrow transplant would have his/her blood type changed to AB (like Eisuke and Rena's case). However if a recipient with AB type blood receives a bone marrow transplant from a donor with O, A, or B type blood, his/her blood would remain type AB, unless the majority of the bone marrow of the recipient is destroyed.
Note that bone marrow transplants do NOT alter the genotype of the recipient. In the case of Eisuke, he is still biologically OO genotype, which means the chromosome 9 he passes to his children still codes for type O blood. If he hooks up with Ran (who has the same blood type as Shinichi whom we've established in another thread CANNOT have blood type AB) their children would have some probability of having type O blood.