Mendel's laws dealt with genes on separate chromosomes. Linked genes are on the same chromosome. Answers will vary but should include DNA samples from parents. Inactivation of the chromosome. Probably mitosis without cytokinesis at about the four cell stage.
Males have only one and it stays active.
Any of several anomalies leading to excess height. Reciprocal translocation b. See page 304. Probably not because this translocation causes reproductive problems. However, it is possible, in which case either parent might also be a translocation carrier. The whole experiment was flawed because Jacobs did not test the non-prison population to see what the incidence of XYY males were found in the general populace.