Personally I'm an Option 2 kinda guy.

I'd wipe everything and start again but that's just how I like to do things and it may not be best for you. My reasoning is that although it should be possible to do things on-the-fly, wiping everything and starting again clears out the cräp, and also reduces the chances of home-made modifications clashing somehow with something else (doesn't really matter what, and there are as many ways for a system to go wrong as there are electrons...) and causing issues either immediately or - even worse - further down the line. So it might actually be simpler to do that.

This is my opinion and it's impossible to quantify how right I actually am. I'm not a Unix guru, but I have half a clue what I'm doing and I'm no stranger to a shell.

Whatever you decide to do, good luck - and let us know how it goes. If you get stuck I'm sure we'll do our best to help. If you do come across any issues, make sure to include as much info as possible, including commands entered into shell or command line, and full output.