Sorry that "boot drive" seems to be foreign concept or word.
No need or way that dust in a 2009 Mac Pro and startup chime would be related.
Zapping PRAM is sometimes all that is needed and that while very old been around for decade plus, SMC Reset if you don't also press the power button while unplugged is not really an effective but is useful.
Power outages, storms and other acts of nature can be harmful if you don't put your equipment, even modem, TV And other devices, running off UPS - they are more than just for power outages.
My trouble is there is learning curve, 20 questions, and no way to know what someone has done, knows, and might have trouble with.
Pulling the drives out is child's play. They are meant for that and is a good first step. And yes Grant is good with making things more English. Even though I taught programming concepts it often took months before new people began to stop thinking a disk drive as memory and yet that is where virtual memory resides.
Stripping the system down you did do, but just not with the hard drive, system drive, boot drive - call it what you want it is where the OS is and boot sequence looks at any and all drives, and a corrupt disk drive can even prevent booting from a DVD OS X Installer at times so removing it is necessary. It is DIY to upgrade and add disk drives and hopefully you have all four drive bays filled with data, backup, system and more.