Why are 2 Mac Pros on a separate subnet directly connected seeing very low transfer rates? I have two Mac Pros and as one is primarily utilized for storage, I thought connecting the two directly under a different subnet would be a worthwhile endeavor that would directly transfer data without having to pass through the switch and therefore augment speed.

Everything seems to work properly in the sense that I can connect via the static IP on the private subnet between the two machines and I likewise I can connect just fine outside of this subnet to the LAN and Internet by the 2nd ports that are connected to the network infrastructure.

Unfortunately, something strange is happening where transfer rates are exceptionally slow.  With the switch I normally get between 70-90 MB/s with AFP, whereas with the a crossover cable connecting them, I'm only seeing &lt; 100 KB/s! 

Any ideas as to what may be going on here?
My first guess would be the crossover cable you're using to connect them. Gigabit ethernet requires a different crossover wiring than 10- or 100-megabit ethernet, and if you have the wrong kind, the computers will either figure out the problem and switch to a slower connection, or just get massive amounts of errors. I don't have 2 Mac Pros handy to check myself, but you can check this in the Network Utility's Info pane: Select the relevant interface from the pop-up menu, then check the Link Speed listed on the left, and the error counts on the right.

If this is the problem, I'm pretty sure the fix is easy too: just use a straight-through CAT-5 (or 5e or 6) cable instead. Pretty much all modern network interfaces do auto-MDIX meaning that the interface can do the crossover internally. Again, I don't have Mac Pros handy to test, but I'm pretty sure their ethernet interfaces support this.