Alien I'm far from the expert here.
I will state that just adding a bunch of fans is not the best answer. Adding side panel fans can disrupt air flow and only use one it absolutly needed. They can be put-off till last because nothing in the case will be in harms way when it is removed to be modded.
Remember that even low dBA fans add up to noise. Something like 3 fans at 28dBA will equal one 33dBA fan. So one good fan properly installed with good air flow will be cheaper and quieter than many low noise fans.
1-With a nibbler the rear 80mm hole can be opened up, then dressed with a half round file if you wish. New holes will have to be drilled to mount a 92mm fan.
You state the grill is removed. Rather than opening up the fan hole an adapter 80 to 92 could be installed on the outside rear of the case or one of the new Silverstone 92mm fans that mounts to 80mm fan holes installed.
I bought my nibbler from Jab-Tech.com because they are supplied direct from Taiwan. This nibbler is a good'en.
2-Blower fan?? Do you mean intake? I have a 114cfm Chinaflo 120x38 that I do not like as it undervoltes with great protest. Send me $8 and it's your's.

I just gave away a Chinaflo 86cfm, 120x38 that's an OK fan that undervolts well on a PWM controller=they are happy together. I have a couple Sanyo Denki 120x39 103cfm@39dBA left F/S that will run near silent at 5V, pushing VG air. PM me if interested.
Blower fan? How much intake do you need. I don't have AC and it gets to 100F where I live about mid-summer. Over 100cfm intake is not necessary.
3-Save the side panel for last.
4-No, imo. If you have only two HDs, mount them to the far left of the cage. This will let the intake air enter with less obstruction. Or, mount the HDs in a three into two cage in the lower 5.25" bays and have no HDs in the cage at the floor of the case.
With this cage empty a sheet of aluminum can be installed that can be bent to direct the intake air up to the HSF. Just a flat piece of thin aluminum bent like a cupped hand. This will kick the intake air up to the Ninja's fan. You can play with it to devide the air so the VGA cooler gets it's fair share. This type of deflector could be modded in with the HDs to the far left. I have no HDs in front of my intake fan.
I read this somewhere. Forgot where.
If your case has a side window air flow can be easily checked using thin tissue on the end of small round sticks. The tissue is hung like tiny flags on the sticks. The sticks are held to the inside of the case window with small balls of sticky modeling clay. Run the case to check flow. Simple! I guess if you still have the rubber darts we all had as kids, those little suction cups would work too
Note: My cases have 80mm blow holes. Wish they didn't. I put very low flow 80mm fans up there.
This is a long post for me......Hope you got something useful out of it.
...Galvanized