I've been on depo for 3 months now and have been experiencing break through bleeding since then. I plan to stop. How long will the break through bleeding last and exit out of my system?

It is hard to predict when the bleeding will stop.  The depo will slowly be out of your system and your cycles will return to normal.   If you are sexually active you should schedule an appointment to start another type of contraception to prevent pregnancy.  

Got my first depo shot on the 2nd of November last year and bled for good 2 weeks then my second shot was due on the 2nd of February so got the Sayana press shot on the 1st of February then I had unprotected sex the next day after the shot, am I protected against pregnancy?

According to your dates, you received your shot on time, and you are not at risk for pregnancy.  ( What does Sayana press refer to??) 

Lately after particularly large stools I have noticed a little blood on the toilet paper. However it was always an insignificant amount so I never paid much attention, I also assumed it may be a tear of sorts from the large stool and was not a large problem. However I noticed more blood than usual after a recent stool, not heaps but enough to leave a noticeable red mark on the toilet paper instead of a faint pink tinge like normal. What does this mean?

From what you describe the bleeding can be from a hemorrhoid or a small tear.  Both occur when people have large and or hard stools.  Increasing water intake and or taking a stool softener can be helpful.  If the problem continues please schedule an appointment with your primary care provider or schedule an appointment at Corner Health Center 

I'm bleeding from mrng 10 to 12 (approximately) with clots and then I don't see any bleeding whole day and night since two days.

Irregular bleeding can be from many different things.    Please schedule an appointmen with your doctor or clinic for further evaluation.  

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