I provided a general purpose name affidavit (for WES ECA) and mentioned and attached the same in my EE/PR applications
It states all the name differences (short form, full forms, misspells etc) across all my different certificates
1) Passport
2) ssc
3) inter
4) btech
5) m.tech
and It mentions that all the name belong to me. in The EE application I used "nickname/alias" drop down and attached the affidavit in the provided section.
Don't worry, most importantly don't waste any time in getting the certificates corrected. Affidavit is all you need.