3 things need to be identified first.
1. What is your desired end-state with the bike?
2. What kind of riding do you do?
3. What's your budget?
Milling the head won't kill the engine fast enough that you should consider not doing it. However, an aftermarket head that uses Pro Design domes is the preferred way to do things. You have 2 options to advance the timing: modify the stock timing plate or buy a flywheel puller ($12-15) and a timing plate. The cheapest gain would be to remove the airbox lid and buy some main jets to get the jetting right, but a Pro Design pro flow kit with your choice of filter is the right way to do things. Alternatively, you can run pods, but again, you'll need to rejet it.