Hi
1) Since you have honestly admitted the details of on going divorce proceedings and 498A cases, ideally it should not be a problem.
2) You will need to provide the entire case details (Petition, Written statement, copies of court proceedings etc) as of date to the consulate.
3) Also since you have been granted anticipatory(not regular bail) bail, you need to check with your lawyer, whether you need any permission from courts in india to travel overseas as in some cases, anticipatory bail conditions are restrictive and prohibits travel.
4) Normally police will insist on regular bail with no conditions attached to issue Police clearance certificate. Please ask your lawyer to guide you on this.
5) One question you need to prepare is that you need to convince the courts in India and the consulate is that you do not have any intention to escape from the judicial process and also that your intention is to return back after completion of your MS program. So you will need to prepare well in advance to answer this query.
Hope this helps