I think I've got this right, just want to make sure with you guys who are more experienced with Linux (Ive never used it). So my plan is to have a USB stick with linux (Ubuntu) on, I will then load bitcoin-qt onto it and only that and have the blocks/wallet on the external HD. I would use Duel boot and have it partition my windows HD but my bios is a bit temperamental and occasionally tries to load drives which aren't there, so dont want to mess with it anymore than I need.
So if I understand you correctly, your plan would be the following:
1) Boot Ubuntu from an USB Stick
2) Install a Bitcoin wallet on Ubuntu
3) Store your wallet files on an external HD that only gets plugged in when you've booted Ubuntu
4) Ubuntu is connected to the internet, allowing you to send transactions directly from your wallet
Assuming you use your Linux installation
only for making BTC transactions
and nothing else this should be fairly secure. Not as secure as taking your private keys completely offline, but short of zero-day attacks it should be pretty safe. I guess the main risk at this point would be you accidentally plugging in the wallet HD while your Windows is running or some similar kind of user error.