1. How I can legally remove my wife from my own (I am husband) flat? I am ready to pay rent to wife.
You can cut electricity, cut water suply and sewerage service.
2. Is it advisable to file Civil Permanent Injuction suite against wife and her parents?
You can file criminal suit u/s 144 CrPC in the district court (Power to issue order in urgent cases of nuisance of apprehended danger). Also can file 406 IPC , 505 IPC and 383 IPC (Extortion)
3. Wife not allowing me to enter in my own house. Is there any criminal case which I can file on wife?
file 406 IPC
4. My main objective is to remove wife from my flat.
You should file speedy trial and prove 498A plaintiff as false to get various relieves.
Please see my profile links for sample petitions and other clues.