1) Yes you can add registration and stamp duty value charges in the cost of new residential house property.
2) Yes you can buy a residential property from the proceeds of commercial property.
3) Yes you need to open CGAS if the entire amount of net consideration from the sale of commercial property is not invested in residential property before the filing of ITR.
4) You can deposit both ways but it should be in CGAS before filing of ITR.
5) There are two options available in your case. One is section 54 EC which allows investment of capital gain in bonds upto Rs. 50 lacs within six months from the date of transfer of property. There is no concept of CGAS under this section.
Other is section 54F in which you can purchase another reisdential property not more than one except existing. In this you need to invest net consideration.