Well, an octad is possible at current prices, I'm sure it won't get more expensive? I'm happy to get an octad now without upgrades and buy upgrades as I need them later. Since it's a system for a long time I want to set it up as high as possible for non-upgradeable parts so I don't have to buy a new Mac Pro later.
Understandable.

Though I'm not sure if it will make it for the same usage for 8 years, unless the software's not updated much between now and then. I'm more accustomed to 3 - 5 years, depending on what it's used for. Then "downline" the system to another, less demanding usage. You could potentially even place it in a cluster.
At any rate, it's a good idea to go with the highest clock speed within budget (but make sure you've current pricing at the time of purchase for RAM and other upgrades you place into the system).
The files are downloaded from the NCBI as single files per chromosome, i.e. 300mb and down to maybe 100-150mb for the smallest chromosomes. The perl script loads the entire file into an array.
I agree, I think the current long load times on my iMac are due to the OS unloading other things from RAM to make room for Perl.
You could try using a single mechanical disk, and see how it performs. Then if necessary, make the necessary upgrades to improve disk performance.
Also, I've no idea what kind of redundancy or availability you may need, given what the system is to be used for (data security and uptime respectively that can allow the system to run, even in the event of a disk failure). I'd need further information to help you with this (if you deem such a data system necessary). This would be accomplished with a RAID card more than likely, though OS X is capable of doing 0/1/10. But parity does require a card.
RAID or not, I'd recommend getting a good UPS, preferably an Online unit, such as a 1500VA unit from APC. You can get them refurbished (saves a notable bit of money), and it will protect the system from power related damage (brown-outs) as well as allow you to shut down safely in the event of a blackout.
Worst case, you could opt for a Line Interactive unit, but it's not as good, nor will it last as long (Online units should last 10yrs or so, before the capacitors go, which can be replaced). It's one of the reasons they're rebuilt and sold as refurbished units, and why there's companies that specialize in this.
Battery replacement is typically 3 - 5 years (I plan on 3 myself), and it's much cheaper to replace them than get a new unit. The Line Interactive are more of a disposable unit if it goes, but it's also cheaper to replace batteries with these as well, assuming it's still functional.
Use a good surge suppressor between the wall and the UPS, as unfortunately, the UPS's surge suppression is typically ~10% on Line Interactive units, slightly higher with the Online units (i.e ~400 J vs. 480 J respectively) of what you need (~4k Joules). Tripp Lite would be a good brand (i.e. IsoTel/IsoBar lines).
I realize this will deduct from the system budget, but it's a seriously good thing to have, assuming you don't already own such items. They're cheaper than a new system, and you won't have the down-time if the system has to go in for repairs due to power related damage (and it's possible they'd figure it out, and deny warranty coverage).