I have a bone-stock, never opened Jasper 512mb internal MU system with a 60gb retail hard drive i got from a friend. 60gb just doesn't cut it anymore, and I want to toss a 250gb in it. I can get the HD for about $45, so my question is, can they ban you? Is there ANY possible way for them to detect it at one point?

If you use a 250GB HD file found on the internet then yes they can detect this. This is because there would be thousands of HDD with the same serial number connected to xbox live at any time.

I don't think they would ever ban you for it though. Pretty much every HDD bought on ebay is fake, so a lot of people who honestly did not know any better would be banned for something they didn't mean to/intend to do.

If i do use that file, is there a way to use a unique serial number?

yes by buying a MS 250GB hard drive and using the serial number from that one without connecting the other drive to any other xbox

Where are you getting the drive for $45?
You really shouldn't worry about it, if Microsoft cared about this then they would already be banning for it. And ask how many people here have flashed hard drives (I do) and haven't been banned (I haven't). Plus, like yaazz said all the 250gb drives on eBay are bulk bough WD drives flashed by the seller (with the same HDDSS.BIN file).

There was a sale at a local computer store that had this hard drive for $45.99 with a MIR but I'm cool with the owner and he said he'd just do it instant. I was planning on just modding it myself.