There was some good info given in the previous thread you started, but here's a few more thoughts:
I couldn't tell if each shelf fills the cabinet, i.e. if you have three separate/independent spaces or if there is room for hot air from each section to move to the very top of the cabinet. This will dramatically impact what you're trying to do. Given your proposed cutout & fan layout, I presume it's the former.
As Wayne mentioned in your previous thread, you still need to get air into the cabinet - the wiring cutouts will facilitate this (unless they're filled with cables), but if the fans just suck air straight up from the cutout you won't be shifting the heated air away from the component. I would consider cutting decent sized holes in the base of the cabinet, and in each of the shelves - they won't be seen, but definitely will help to get airflow across each piece of equipment.
As an aside, the fan + cutout orientation in your current design is incorrect - hot air rises (!) - which may be one of the reasons you're changing things around.
To address your specific questions:
1. Not sure if the cutouts are going to be a problem - what you need to ensure is that you do have airflow across the equipment and this means having a way for cooler air to enter the enclosure at the right location(s).
2. Six 120mm fans does feel like overkill, but you may be intending to dial back their speed to reduce noise - a "big" fan running slowly will be much quieter than a small fan running flat out.
3. Again, Wayne's suggestions in the previous thread were sound - you've got to allow cooler air to be drawn into the cabinet from somewhere: your lowest cutout might suffice, but only if the shelves don't interfere with the upward movement of air. not sure if you saw it, but I posted a link to a document from Middle Atlantic in the old thread that does a really great job of explaining what you need to be thinking about. [http://middleatlantic.com/pdf/ThermalManagement.pdf
- some of the text gets a bit heavy-going, but just look at the diagrams - they show exactly what you need to be aiming for,.... and what you should avoid doing.]
4. Nope - always put the components that generate most heat on top, and then sequence them in descending order of thermal output. This typically means amps (or maybe the PlayStation) at the top - not always ideal from a convenience or accessibility perspective, especially with a floor-mounted cabinet, but it is important if heat is an issue.
Not sure if any of this helps, but just focus on allowing cool air to enter the cabinet and having a good flow across each piece of equipment - I get the sense that what you're proposing still doesn't quite feel like it does this.