Nepal

Hi Ajay,
If you have not done Bachelor's degree, you have to write to them and ask them if CA qualification will be enough and will be considered as an undergraduate course or not.

There are many institutes that take in a lot of students from Nepal.These colleges need to be contacted to get your documents verified before you opt for admission.
For example, Manipal University, Christ University, etc.

Hi,
One cannot really predict the visa chances. Your grades are good. To increase visa chances, apply to an university on time and show confidence in your application and profile. Very good English skills are required. You must be clear with your career plans. Your visa can also get rejected if you show any plans of migrating.

Hi,
You need to check with Tribhuvan University, Nepal about this. Otherwise, most of the colleges accept Amity University's MBA degree.

You are eligible to seek admissipn in BBA in Indian Universities and Colleges. You may a list of colleges you want to target and make a plan how to seek admission by going through thier websites.

BE and B.Sc agriculture are totally different courses.

You may refer to list of Universities whose Engineering degree is recognised by Nepal Engineering Council: http://edusanjal.com/blog/list-of-indian-universities-recognized-by-nepal-engineering-council
YMCA University is not in above mentioned list.

Where in Nepal is more important? The bigger the city, the better the exposure and faculty quality. I can't give a generalized answer regarding whole of Nepal. If it is Kathmandu then it is better but if you compare Delhi with Kathmandu, any day Delhi will be better.