Exam

We have to convince the dean and pay 600 to attempt missed exams.

First we have to give a leave letter, if the sir accepts the reason he will retake the exams for all absented students.

Congratulations for your rank, you can easily get lower branch of NITs from north east. 

ie.

NIT Sikkim

NIT Meghalaya

NIT Mizoram

NIT Agartala etc.

It's difficult to get any government college with this percentile but here are some colleges for which you can try- 

1. Keystone School of Engineering, Pune
2. KKEI'S Trinity Academy of Engineering, Pune.

As It is mostly depandent on 12th percentage and JEE main mark (sastra will calculate like this 12th percentage * 0.75+jee main mark * 0.25)

As you have already got 98.6% in boards, hopefully you will get CSE in Sastra University.

According to me, going for the direct admission in BT.ech CSE would be a better option since you have good percentile in JEE mains. Thanks

Your rank is quite low so it might be difficult for you to get into government colleges for B.Tech but you can target the private universities and some other state universities. All the best

Yes, you have some chances of getting into NIFt with 1542 reserved category rank but it may depend on the number of seats available in the particular university. 

You will have to report to the dean/controller of examination and if your reason is found genuine, then there won't be an issue. If you miss the internal exam they re-conduct internal exam so you can appear in that. But end semester exams are main and if you miss or fail any in any subject in that exam you fail the whole semester and you'll have to re appear for that subject in next alternate semester. Internal marks are also important as they make overall GPA of the semester.