You should be fine, providing as you say its the only thing the system is doing.
From the POV of the CPU you might want to run multiple processes simultaneously to speed things up if that's a bottleneck. More relevant to your question though - a CPU will throttle and self protect if it gets to warm, so the system will protect itself just fine from a CPU POV.
From a RAM POV I doubt this will make a difference.
From an HDD POV, if drives are going to die they are likely to do so anyway. I doubt the slight reduction of heat will make a significant difference. Also bear in mind that startup is heavier on wear and tear them just running a process. If it were me I would not worry, or put a couple of fans blowing over the disks.
Doing high load task for a few days is well within the ability of any decent server - I'd just let it run.