For the trans, you may need to boost line pressure/shift firmness via a tune. If it shifts somewhat firmly still then you should be fine with a medium shot, say 75, and the progressive controller. If you desire, you can actually set the window so the nitrous turns off prior to a shift, and re-ramps when your RPM's drop back down into the window going into the next gear. Never hurts to have a spare transmission around though that's built for the job (or at least the money for one set aside). Its a matter of time before it quits no matter how careful you are.
Make sure your car is delivering the fuel pressure. Can't stress that enough. Hopefully someone with experience with this on a Mark can chime in let us know what the stock fuel system is capable of supporting. A search might show that as well. How big do you plan to go?