You will need a comparison program like Beyond Compare - I don't travel anywhere in vB-world without my PHP files set to open in Beyond Compare
Process:
1] get all your current vB fles downloaded into a fresh backup folder
2] extract the upload folder of your vB 3.0.3 to a clean folder
Now - do side by side comparisons of each file - any changes associated with hacks you should re-apply to your new 3.0.3 files.
3] stop your forum to retain integrity
4] create and download a fresh backup of your forum database
Upload your modified files, then run install/upgrade.php
5] most large hacks will have provided facilities to re-install templates if they have originally been installed into the MASTER style (this i feel is a kinda painful way to install tempaltes - I prefer to install templates into all styles that have no parent, but are NOT styleid = -1 - that's my AUD$0.02c)
Now you should be back up and running

restart and then test everything