Hardware troubleshooting

I have been having some problems lately with my most important server. I believe the SATA controller on the motherboard is faulty, as all disks see read or write timeouts when the heavy backup scripts run overnight, and sometimes during the day as well. I do not appear to be having corruption issues, at least not yet. Apache has crashed a few times, and I've seen issues with directories being not found, despite them in fact being there.

Before I waste money on an add-on SATA controller or other parts, how can I approach isolating this problem? I could see a bad stick of RAM causing this kind of problem as well, so I'd like to cross that off the list, along with anything else.

What tools are best to use, either in FreeBSD or standalone, that I can use to test various hardware related to my main problem? I'd like to avoid things like make buildworld as it would not isolate my problem.
 
If you have the backup scripts with rsync, you can use its bwlimit parameter (see my other threads with that term). Sorry cannot answer anything else knowledgeably.
 
@Pushrod: have you verified (by looking at the system logs - /var/log/messages to be exact) that you server isn't runing out of swap? Running out of swap will kill programs.
 
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