Long story, frustrating Vista/hardware problems, please help.

Okay, I'm going to try keep this concise, but I've been up well over 24 hours and am extremely irritated; be warned I may ramble.

Built my mother an E4400, MSI P965 Platinum system awhile back with OEM Vista Home Premium. For awhile now it's had its share of problems, but recently they became too many and too severe to do anything but reformat. Issues included: ridiculous several-minute boot up, no sound in Media Center, wireless internet only working when it wanted to and at a snail's pace when it did, oddly slow and inconsistent transfer speeds to some USB hard drives, plus a myriad of other quirks and slowdowns that led me to believe it was just an old and buggy Windows install. The only issue that said "hardware" to me (other than the transfer speeds) was the ludicrously long POST screen. I can't see how that would be affected by anything on the hard drive/Windows install when it occurs prior to boot and at the motherboard/BIOS level.

The reinstall of Vista went smoothly, the only hiccup in the first six hours of updating and installing drivers/apps was at the very beginning when the Netgear utility would instantly close upon opening, but a reinstall cured it and it didn't have any other issues within the first 20 million reboots this process requires. Everything was perfect, even the POST screen was snappy. But here's where it you have to start paying more attention.

Apparently the issue does not lie in any of the core hardware. After the last perfect bootup one of two things fusked it all up:

First, I had setup Media Center for recording TV with a Hauppauge WinTV-PVR-150, and second I put some programs from my computer on an SD card and when I inserted the SD card... lock-up. This had occurred before, but I thought the SD card was to blame, now I know it's the reader. But the worst part is that upon restart... excruciatingly long POST screen and boot-up again! When it finally entered Windows, the Netgear utility started acting up again, and the computer in general started displaying its old quirks I had just spent 7 hours (on and off) fixing.

It seemed like putting the SD card in the faulty reader was to blame, but how could that possibly piss all over the Vista install and affect POST times permanently when it had been in there all along? It seems like whatever issues that would cause would be more hardware related and would not be fixed by a reformat.

So then I leaned toward the hardware configuration with Vista not liking the tuner. I can grasp that causing software issues and long boot times, which this setup has had long before the card reader went defunct, but the POST times is still beyond me.

Tomorrow I plan to pull the card reader and test, and then the tuner, which you're probably saying I should of tried before posting this long ass post. But my main concern is that even with both pieces removed, the problems will persist and I'll have to reformat again (luckily with no downloading this time), but I really, really don't want to reach that point again of setting up Media Center and recreating the issues, while at the same time I don't want to just assume it's the tuner and waste money on a new one. So if someone experienced could please give me a confident, educated opinion on what's going on I would appreciate it so I don't waste any more of my time.

(Or hopefully pulling the reader and/or tuner will fix it and this post was the biggest waste of time.)

Yes, two gigabytes, and USB devices are victims of the strangest problems.

I forgot to mention that a little USB key that she keeps in there for backups used to try to boot when the boot order didn't specifically have the hard drive before USB legacy devices. Well, that wasn't happening post-format until the crash.