Defrag and all of that is not going to fix corruption in your operating system. Defrag moves blocks of data around to make them contiguous on the drive. Chkdsk checks for PHYSICAL issues on the drive first, then LOGICAL issues, but only as those issues relate to where the next byte of data is. It will not fix dirty files, and if your OS has corruption, only a clean reinstall will fix it. There IS a repair, but that's on the black diamond slope and not for novice skiers.

As far as using the small drive in the full sized tower, there are conversion kits that are rails you screw to the mini drive and then screw the rails in where the 3.5" drive would normally go. To be honest, I have used those drives with double sided carpet tape with no ill effects.

Honestly, I do not like Asus and would jump on the pile and suggest you return it. I am curious to know this, but I suspect you chose Asus because it was cheaper than other brands. Remember, cheaper doesn't necessarily mean less expensive. Can you put a price on the aggravation you have already gone through?