The usual way people upgrade between revisions is to buy the newer revision, shift any hardware over that they want to keep (like a high-end graphics card), wipe the drives & reinstall MacOS X, and put the old machine up for sale locally or on eBay. Unless you live nowhere near a major metropolitan area, you won't have issues reselling the machine if you want to. Every time there's a new model, you usually see a bunch of folks selling their old systems.
The logic board may be interchangeable between different systems, but you're flying in unknown territory with that one - the logic board is tightly integrated with / customized to a lot of other components in the chassis (front panel controls, power supply, etc.)
Since Apple only sells parts to Apple Authorized Resellers and their technicians, your only option for purchasing a logic board (or replacement non-standard PC components) would be through ebay or a handful of used-mac-parts companies (like iFixit.) They buy new or used systems and disassemble them for parts.
CPUs on systems with socketed processors have some upgradeability; people have upgraded their Mac Pros this way (some Mac Minis and iMacs also had socketed processors, too) and documented as such on the usual Mac-related web boards/forums. This is expensive on the Mac Pros, given they're Xeons.
There should be no need to upgrade the power supply; they're reliable and designed to handle the maximum capabilities of the machines, which include some pretty 'big' GPU configurations. No, you can't pop an ATX supply in.
Depending on which generation of Mac Pro, the memory is specialized; some take FB-DIMMs. There have been reports that some aftermarket ram modules don't work well in some Mac Pros (temperature/heatsink issues), but a major manufacturer/reseller like Crucial should supply working memory.
Drives are completely standard SATA. Same with CD/DVD-ROm drives (verify the drive model works with OS X first.) There's an optional hardware RAID controller card that's probably not worth it. Areca, Adaptec, and others make compatible RAID controller cards; if bootability is important to you, check on this, as not all of them are.
Graphics cards are standardized for the most part (save some which have custom connectors; for example, mine has a DVI port and a mini-displayport.) The question is compatibility with MacOS X, but there are a very large number of compatible cards, and the Hackintosh community has pretty thoroughly documented that one for you already.
Sidenote: consider an iMac. It can drive a second display out of the box, they have a second internal hard drive bay, the i7's are as fast or faster than the Xeons in some applications, and they're a LOT cheaper than a Mac Pro; probably quieter and use less power, too. Spend the $ on more memory or an SSD, etc - an iMac with an SSD will wipe the floor with a Mac Pro without.
You're better off using an Mac-supported cards from Apple or others.
Apple's card are seriously outdated, both 5770 and 5870 are slow card in today's standard.
There "should" be a renew of Mac Pro some day, you can wait for that.
There are a cards like the Quadro K5000 that is Mac-compatible. But NOT out of the box. You need to install the driver first, and then install the card.
Also, support for AMD HD 7 series cards ARE NOT IN YET in 10.8.2. I had one of those in my old Hackintosh running 10.8.3, and it's still recognized as "AMD Radeon HD 7xxx series", so I will say wait for it.
Don't make any moves before AMD 7 series is out, maybe Apple or third-party will release cards for it.
Good luck!
Best Answer
The CyberPower rep is only partially correct:
Mac Pro Power Efficiency
Apple puts out an excellent document (PDF) on the efficiency of the Mac Pro. But specifically, it get a 90% power efficiency rating at 100V, 115V and 230V which far exceeds the 85% minimum threshold set by the EPA to be Energy Star v6.0 compliant
From EPA Energy Start requirements:
Apple Power Supplies
Apple's power supplies from the base model MacBook to the top of the line iMac Pro all use power supplies with high efficiency
To achieve this level of efficiency, this basically requires PFC. Looking at a tear down of a MacBook power adapter, we can see the PFC circuitry.
So, bottom line is that your Mac Pro has a PFC power supply
UPS with sine wave output.
Unless you are running sensitive (and that being the operative word) equipment that will react badly to non-sine wave or simulated sine wave power output, you have no need for this. By sensitive, I mean things like scientific instrumentation, network communication gear (telco), high-end audio electronics, etc.
Apple's products are robust enough to withstand the fluctuations in standard UPSes and from the electrical grid.
From personal experience, I have used UPSes (Uninterrupted Power Supply) from APC and CyberPower purchased at the local big box store on sale; and as a resident in FL with frequent power outages during the summer months, neither have failed to keep my computers (Apple, Dell, Synology, etc.) running without issue.
TL;DR
Yes, you have a PFC (Power Factor Corrected) power supply. All Apple computers have a PFC power supply.
No. You don't need a “sine waveform UPS”. It will not hurt to get one, but your benefits will be negligible; a standard UPS will work fine.
It's likely the rep is reading a Feature/Benefit chart and attempting to up-sell you on a product you don't really need.