Bestofluck:
After reading your post, I feel I will be in problem!!!
LoE 1: Explaining my company does not give Ref letter on letter head. Hence submitting the Ref letter from Manager on plain paper, notarized
with his business card.
Well, may be your company is hesitant to issue the letter to existing employees but they do issue it to former employees. But in any case, it's a Global leader with presence in Canada as well so may be that should help your case in some way. Hopefully, you would have submitted Joining letter, Annual appraisal letters, salary slips etc. If you get any doc. request don't forget to include scans of your IT certifications as well.
LoE 2: PoF. My parents gift deed, affidavit, cheque copies
If money is constantly there in your account as per last 6 months statements, IRCC tends to accept it as yours so PoF would not be a problem
LoE 3: Submitting master, bachelors degree copies and transcripts
Submitting due to requirement difference between OPNP application form versus Application guide :'( :'( :'(
ECA is all they need. Degree, marksheet are just for completing their file formality