Did the pull-out method fail me? Late period.

Since you took the morning after pill multiple times within a month may have altered your menstrual cycle and caused a delay in your period. But there is still a possibility of pregnancy even if you have taken the morning after pill. Because emergency contraception is not 100% effective in preventing pregnancy, and repeated use of the pill within a short period of time may decrease its effectiveness.

Menstrual bleeding patterns often change when hormonal tablets are administered. But, if your menstruation continues for too long than usual then medical help of a gynecologists is required.

Its a rare congenital condition that occurs during fetal development. Generally most congenital abnormalities including penile agenesis are not preventable. They can result from a combination of genetic, environmental, and developmental factors that are often beyond our control.
It is also important to seek emotional support and counseling to address the feelings and challenges you may be experiencing.

If you took a double dose of the pill on a single day and then accidentally didn't take it for two days, keep in mind that the contraceptive pill will not be as effective as usual if you miss some, though. You may notice a spot, sometimes bleeding, or a conception of pregnancy in your body. In the interest of safety, take your pills at the same time every day and, in case of doubt, use additional protection with prevention against sexually transmitted diseases like condoms for the next seven days. 

Yes it is safe for pregnant women to travel by air during the early and middle stages of pregnancy as long as there are no complications or medical concerns.