i m not expert but as per my research & my location on my plot coz I m also building new home for myself ur puja room shud be in northeast so that while worshipping u shud face towards east.
answer to ur query1. is u shud consult an architect coz the way u gonna construct is not good coz u r wasting too much area consult an architect so he will help u building the floor plan as per laws
2.borewell & underground is fine but lift & stairs shud b in south east coz that is the negative zone..
3.puja room shud not touch any toilet walls as per vaastu
4.wardrobe is ok behind pujaroom
5.location of toilet shud not be in center of building as per vaastu so try either front or back & bedroom shud be located as such that while sleeping ur head shud not be at north side.
if interested can send u a better plan let me know where u from n how much area u want to cover