For my friend, since he has the RPC-24 we even spaced out the drives and left the 1U rackspace above and below the server open. Problem solved!
Leaving the space above and below open is generally a bad thing. It's dependent on specifics of course, but you should consider the following:
A server chassis is designed to cool front-to-back (usually), and in a stack with other servers. While some heat will of course dissipate up and down, the vast majority of BTU's should be heading out the back. Any BTU's that dissipate to the next server down or up have to be dealt with by that unit's cooling system, and that suggests that other units are heating the unit that we're discussing, so in reality it should all kind of be a wash anyways. All of the units are moving the heat from the front to the back.
If you introduce gaps, you've just introduced a complication. Now you have stagnant air zones; if you are truly pouring BTU's out the top (and bottom) of your server, then you are creating an artificially hot zone above (and below) your server. You're heating it up. The heat sits there. Your server has to get warmer in order to continue dissipating heat in that direction. Good? Probably not.
Now, if you have a stack of crappy servers, all of which are insufficiently cooled, stacking them without gaps will cause them to bake. Gapping them might make them bake somewhat less; the evidence for this is nonconclusive.
However, if you have a stack of decent servers, stacking them without gaps helps to guarantee that the fans on surrounding units will help keep a unit with malfunctioning cooling at a better temperature than it would otherwise; the BTU's don't get to go heat an air pocket inbetween the servers.
So, if you've followed this so far, you're quite possibly saying "but my friend doesn't have any other similar servers, it's just this one." That's fine. It doesn't change the reality of it all. You already figured out that staggering the drives in your server helps them run cool. That's because your server has some airflow, and it is distributed more evenly when you stagger things out. What I'm saying is that this probably isn't true of the gap above and below the server. You really want the air moving there so there's less heat buildup.
So it'd be really much better to go and identify your BTU load and make sure your server cooling design is adequate for that plus a healthy margin, then you can eliminate the EZ-bake oven zones around the server.