1) Correct your passport to your correct name. Possibly to your PG certificate (though the initials may be complicated)
2) If your PG certificate is a master’s (and you are confident WES will accredit it as such), you can exclude your bachelor’s altogether and simplify your life a bit
3) Get a same name affidavit for two or three names (you can look up how it’s done in your particular jurisdiction)
As I see it, while your immediate issue is the ECA, you ideally want as much consistency as you can get to make the PR and future procedures simple. In your place, I would pick the “right name”, then go about correcting ) officially explaining any deviations. On a personal note, I had a name mismatch between my high school diploma and my passport. Got my passport changed then, and subsequently made sure I used the same name for everything.