1. Most monsoonal research is focused on explaining the monsoonal passage through the plains of the Indian subcontinent. Very few papers can be found on how the same troughs cause rainfall at 3000 meters. I would like an authoritative reference on Monsoonal Mountain Meteorlogy. All that is known is that the MJO (BSISO) troughs and ridges at the 850 hPa seem to be damped at the Himalayan foothills.
2. Regarding the 500 hPa propagating downwards I cannot get further more information than introducing the concept of a downward propagating Rossby wave. And as far as the physics that explains what happens when these two disparate systems meet it is at best an open research topic.
3. I have read recent discussions(no reference available yet) that the two systems may need to "line up" in other words the geometric center of the upper level system needs to pass through the center of the lower level trough.Very recently Tropical Cyclone Hudhud moved up northwards towards the Himalayas and caused a blizzard in Nepal. There was a corresponding mid latitude disturabance at around the same time over the western Himalayas but extraordinary damage was prevented because the two systems did not line up.

What is of more serious concern is the fact that there have been four such incidents in recent times - 1) Pakistan Floods 2010 2) North Indian Floods 2013. 3) Indian Pakistan floods of 2014. 4) The near miss with Cyclone Hudhud. What climatic changes are causing these collisions between disparate systems is a new field of study. Both weather and climate models will be stretched to predict these sort of collisions.