Premiere sucks for automation
You can't define every clip to NOT de-interlace on slow down, keep aspect ratio(tho you should be working with a file that doesn't match the ratio of your project) or set pixel aspect ratio...no you have to set setting each time

. Well if you do it from the bin window first then it applies it to cuts you make later on. Anyways.
You wanted a stoby effect with a fade in fade out ?
Seems to me you'd render your clip with strobes, export that clip, then import it again and setup the rubberbands for a fade-in / fade-out effect. Or you can juse use the strobe effect with the rubber bands.
As for applying this to each clip you're probably going to have a HARD time doing so as clips that don't match the size of the original probably aren't going to turn out properly and you'll have to manuall adjust them
~klinky