If you're willing to hear a little crazy talk, I've had a few thoughts.
Firstly, I think you're on the right track with more intake fans than exhaust, considering the size of area above the IO ports - you're not going to fit a reasonable fan in there nicely. I think there are a few options, though, once you cut away as much metal as you reasonably can from that area:
Rely on the pressure from the intake fans to move air out there, as there will be little resistance in that path.
Or, depending on how good your metal work skills are (or how 'ghetto' you're prepared to have the case looking) create a simple duct from the opening out to an externally mounted 120mm fan.
I'd probably go the 'duct' route, if I was in your position, but I enjoy making cardboard contraptions
Secondly, you've shown a single 120mm fan on the front panel, but is there any particular reason you couldn't use two? How many drives are you planning to mount in the case? If you're planning a few, would you consider relocating their cage to, for example, the bottom of the case? This would allow a second 120mm fan on the front panel and improve your intake situation.
Finally, this case is absolutely /begging/ for a PSU chamber! You're replacing the PSU, which probably means you'll end up with one with a large fan in the bottom; this is fine. Mount it upside down in the PSU area [bear with me] and create a top chamber in your case by blocking off any openings into the top area. The intake for the PSU will now be through the front panel 5 1/4" bays, which you could either leave open or block with something that will allow the PSU to breathe. Obviously, you'll still need to get power cables into the lower chamber. The benefit of doing this is that your PSU will stay cooler, by only getting near ambient temp air, which helps it stay quieter. It can also mean that the PSU stays in the more efficient regions of its power curve.
So, to recap, try for 2 intake fans on the front panel. Consider separating the PSU chamber from everything else - if you're keen, consider how you could install all your drives up there, out of sight and cooled by roughly ambient air. Finally, rely on the intake fans to generate front to back airflow, and open up the back of the case as much as possible. If you go for 2 intake fanse, you could even compartmentalise further and have the lower one feed air into a GPU/expansion cards 'compartment' and the upper fan feed air across RAM and CPU. You'd need to remove any expansion area blanking panels you didn't need in order that the warm air had somewhere to move to.